9BDT: Apolipoprotein B 100

Apolipoprotein B 100 bound to LDL receptor and legobody. Determined by electron microscopy at 5.4 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 5.4 Å
Organisms: Homo sapiens, Mus musculus, Escherichia coli
Chains: 7
Atoms: 38,899
Mol. weight: 831.62 kDa
Ligands: CA, NAG
Released: 25 Dec 2024

Explore 9BDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BDT contains 119 α-helices and 399 β-strands across 7 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 76 helices, 290 β-strands

Element	Residues	Length	Sheet
β-strand	50-57	8	1
β-strand	59-63	5	2
β-strand	72-73	2	2
β-strand	77-84	8	1
β-strand	91-94	4	1
β-strand	100-101	2	3
β-strand	114-115	2	3
α-helix	119-124	6
β-strand	131-132	2	1
α-helix	136-138	3
β-strand	144-145	2	1
α-helix	151-164	14
α-helix	167-169	3
β-strand	174	1	4
β-strand	177-181	5	5
β-strand	184-188	5	5
β-strand	191	1	4
β-strand	203	1	6
β-strand	204	1	4
β-strand	207	1	5
α-helix	213-215	3
β-strand	228	1	7
α-helix	235-238	4
β-strand	239	1	8
β-strand	242	1	9
β-strand	243	1	5
β-strand	246-248	3	6
β-strand	258-260	3	6
β-strand	264	1	9
β-strand	267	1	8
α-helix	272-274	3
β-strand	279-283	5	2
β-strand	286-287	2	6
β-strand	290	1	1
β-strand	293	1	1
α-helix	325-338	14
α-helix	344-356	13
α-helix	360-365	6
α-helix	367-373	7
α-helix	375-382	8
α-helix	388-401	14
α-helix	405-415	11
α-helix	423-436	14
α-helix	441-453	13
α-helix	461-474	14
α-helix	482-500	19
α-helix	504-506	3
α-helix	508-515	8
α-helix	521-531	11
α-helix	540-549	10
α-helix	555-565	11
α-helix	571-583	13
α-helix	587-602	16
α-helix	609-612	4
α-helix	616-619	4
α-helix	623-625	3
β-strand	637-639	3	10
β-strand	643-645	3	11
β-strand	648-651	4	11
β-strand	655-660	6	10
β-strand	670-678	9	10
β-strand	684-693	10	10
α-helix	697-704	8
α-helix	712-716	5
α-helix	761	1
α-helix	762-766	5
α-helix	769-771	3
β-strand	774	1	12
β-strand	778-779	2	13
β-strand	782-783	2	13
β-strand	788	1	12
α-helix	789-806	18
α-helix	809-813	5
α-helix	815-818	4
β-strand	826	1	14
β-strand	829-833	5	7
β-strand	837	1	7
β-strand	845-854	10	7
β-strand	857	1	14
β-strand	858-861	4	15
β-strand	870-877	8	15
β-strand	879-890	12	7
β-strand	901	1	7
β-strand	905-907	3	7
β-strand	912-918	7	15
β-strand	921-923	3	15
β-strand	926-927	2	16
α-helix	928-929	2
β-strand	933-936	4	17
β-strand	939	1	17
β-strand	943-945	3	18
β-strand	950-952	3	18
α-helix	953-956	4
β-strand	960-970	11	17
β-strand	973-982	10	17
β-strand	1000-1007	8	17
β-strand	1013-1014	2	16
β-strand	1017-1018	2	19
β-strand	1022-1025	4	20
β-strand	1028-1031	4	20
β-strand	1033	1	21
β-strand	1035-1036	2	19
β-strand	1051	1	21
β-strand	1073-1078	6	22
β-strand	1095-1100	6	22
β-strand	1105-1110	6	22
β-strand	1118	1	23
β-strand	1120-1126	7	22
β-strand	1131-1134	4	22
β-strand	1136-1139	4	23
β-strand	1148-1151	4	23
β-strand	1154-1156	3	22
β-strand	1159	1	22
β-strand	1165	1	23
β-strand	1166-1168	3	24
β-strand	1175-1182	8	24
α-helix	1187-1192	6
α-helix	1199-1212	14
β-strand	1279-1287	9	24
β-strand	1355-1361	7	24
β-strand	1368-1376	9	24
β-strand	1389-1394	6	24
β-strand	1401-1407	7	24
β-strand	1418	1	25
β-strand	1423-1428	6	24
β-strand	1433	1	26
β-strand	1435-1436	2	24
β-strand	1437-1438	2	27
β-strand	1441	1	28
β-strand	1443	1	25
β-strand	1449	1	28
β-strand	1450-1456	7	27
β-strand	1457	1	26
β-strand	1466-1472	7	27
β-strand	1476	1	29
β-strand	1479	1	29
β-strand	1481-1486	6	27
β-strand	1489-1491	3	27
β-strand	1496-1498	3	27
β-strand	1500-1506	7	27
β-strand	1514-1517	4	27
β-strand	1520-1521	2	27
β-strand	1529	1	30
β-strand	1534-1537	4	27
β-strand	1538	1	31
β-strand	1541	1	31
β-strand	1544-1545	2	32
β-strand	1550	1	30
β-strand	1556-1558	3	33
β-strand	1560-1563	4	32
β-strand	1568-1571	4	32
β-strand	1573-1575	3	33
β-strand	1584	1	34
β-strand	1585	1	33
β-strand	1588-1590	3	32
β-strand	1597-1599	3	32
β-strand	1603	1	34
β-strand	1617-1618	2	32
β-strand	1625	1	32
β-strand	1626-1629	4	35
β-strand	1640-1647	8	35
β-strand	1652-1661	10	35
β-strand	1666-1668	3	35
β-strand	1674-1676	3	36
β-strand	1679-1681	3	36
β-strand	1682-1688	7	35
β-strand	1695-1703	9	35
β-strand	1708-1712	5	35
β-strand	1715-1716	2	35
β-strand	1723-1727	5	35
β-strand	1730-1732	3	35
β-strand	1735-1744	10	35
β-strand	1750-1752	3	35
β-strand	1754-1760	7	35
β-strand	1764	1	35
β-strand	1767-1775	9	35
β-strand	1778-1785	8	35
β-strand	1787-1789	3	35
β-strand	1792-1795	4	35
β-strand	1797-1803	7	35
β-strand	1806-1817	12	35
β-strand	1820-1831	12	35
β-strand	1834-1845	12	35
β-strand	1848-1857	10	35
α-helix	1859-1861	3
β-strand	1865-1873	9	35
β-strand	1876-1885	10	35
β-strand	1892-1894	3	35
β-strand	1897-1899	3	35
β-strand	1905-1916	12	35
β-strand	1923-1935	13	35
β-strand	1940-1953	14	35
β-strand	1959-1968	10	35
β-strand	1971	1	35
β-strand	1980-1981	2	37
β-strand	1983-1987	5	35
β-strand	1990-1991	2	35
β-strand	1992-1993	2	38
β-strand	1996-1998	3	37
β-strand	2007-2009	3	37
β-strand	2012-2013	2	38
α-helix	2036-2040	5
α-helix	2043-2047	5
β-strand	2065-2069	5	39
α-helix	2074-2083	10
α-helix	2085-2100	16
α-helix	2387-2389	3
α-helix	2390-2405	16
α-helix	2409-2428	20
α-helix	2432-2435	4
α-helix	2438-2440	3
α-helix	2441-2456	16
α-helix	2459-2468	10
α-helix	2737-2739	3
α-helix	2745-2747	3
β-strand	2750-2754	5	39
β-strand	2758-2762	5	40
β-strand	2765	1	40
β-strand	2769-2777	9	40
β-strand	2788-2789	2	41
β-strand	2791-2799	9	40
α-helix	2802-2804	3
β-strand	2806-2811	6	40
β-strand	2814-2815	2	41
β-strand	2823	1	40
β-strand	2826-2830	5	40
β-strand	2835-2845	11	40
β-strand	2850-2860	11	40
β-strand	2861	1	42
β-strand	2866	1	42
β-strand	2867-2877	11	40
β-strand	2880-2882	3	40
β-strand	2886-2895	10	40
β-strand	2900-2906	7	40
β-strand	2909-2910	2	40
β-strand	2913-2915	3	40
β-strand	2918-2920	3	40
β-strand	2923-2932	10	40
β-strand	2941-2951	11	40
β-strand	2954-2964	11	40
β-strand	2968-2976	9	40
β-strand	2984-2994	11	40
β-strand	3000-3008	9	40
β-strand	3015-3023	9	40
β-strand	3026	1	40
β-strand	3030-3042	13	40
β-strand	3045-3060	16	40
α-helix	3061-3063	3
β-strand	3064-3078	15	40
β-strand	3084-3089	6	40
β-strand	3092-3093	2	40
β-strand	3096-3097	2	40
β-strand	3100-3105	6	40
β-strand	3112-3117	6	40
β-strand	3120	1	40
β-strand	3121-3122	2	43
β-strand	3131	1	44
β-strand	3148	1	44
β-strand	3166-3167	2	43
β-strand	3171-3175	5	40
α-helix	3192-3230	39
α-helix	3231-3233	3
α-helix	3238-3240	3
β-strand	3245	1	45
α-helix	3248-3252	5
β-strand	3258	1	46
α-helix	3260-3262	3
β-strand	3265-3267	3	45
β-strand	3275-3279	5	45
β-strand	3284	1	47
β-strand	3285	1	46
β-strand	3291	1	47
β-strand	3296-3298	3	45
β-strand	3339-3343	5	40
β-strand	3349	1	48
β-strand	3350-3355	6	40
β-strand	3365-3370	6	40
β-strand	3371	1	48
β-strand	3379-3384	6	40
β-strand	3401-3403	3	40
β-strand	3408	1	40
β-strand	3409-3410	2	49
β-strand	3422-3423	2	50
β-strand	3427-3429	3	49
β-strand	3436-3445	10	49
β-strand	3446-3447	2	50
β-strand	3454-3464	11	49
β-strand	3466	1	49
β-strand	3471-3485	15	49
β-strand	3490-3499	10	49
β-strand	3501-3504	4	49
β-strand	3507-3509	3	49
β-strand	3512-3521	10	49
β-strand	3526-3535	10	49
β-strand	3538	1	49
β-strand	3542-3550	9	49
β-strand	3552-3554	3	49
β-strand	3559-3562	4	49
β-strand	3564	1	49
β-strand	3567-3573	7	49
β-strand	3577-3583	7	49
β-strand	3584-3587	4	51
β-strand	3588-3590	3	49
β-strand	3592	1	52
β-strand	3595	1	52
β-strand	3600-3603	4	51
β-strand	3606-3607	2	53
β-strand	3612-3613	2	53
β-strand	3618-3624	7	51
β-strand	3629-3638	10	51
β-strand	3642-3652	11	51
β-strand	3657-3667	11	51
α-helix	3671-3674	4
α-helix	3684-3687	4
β-strand	3700-3705	6	51
β-strand	3708-3712	5	51
β-strand	3724-3725	2	54
β-strand	3730-3731	2	54
β-strand	3733	1	55
β-strand	3737	1	56
β-strand	3740	1	56
β-strand	3750	1	57
α-helix	3756	1
β-strand	3757	1	57
α-helix	3758-3759	2
β-strand	3767	1	55
β-strand	3770	1	54
β-strand	3773	1	58
β-strand	3779-3780	2	59
β-strand	3790-3791	2	59
β-strand	3797-3798	2	58
β-strand	3813-3814	2	58
β-strand	3821	1	59
α-helix	3844-3847	4
α-helix	3856-3858	3
β-strand	3880-3885	6	51
β-strand	3887-3890	4	51
β-strand	3894-3904	11	51
β-strand	3908-3919	12	51
β-strand	3926-3937	12	51
β-strand	3940-3951	12	51
β-strand	3955-3960	6	51
β-strand	3963	1	51
β-strand	3971-3973	3	51
β-strand	3976-3979	4	51
β-strand	3987-3988	2	51
β-strand	3991-3992	2	51
β-strand	3996-3998	3	51
β-strand	4001-4003	3	51
β-strand	4007-4014	8	51
β-strand	4021-4027	7	51
β-strand	4036-4043	8	51
β-strand	4046	1	60
β-strand	4051	1	60
β-strand	4053-4057	5	51
α-helix	4060-4068	9
α-helix	4073-4088	16
α-helix	4089-4093	5
α-helix	4097-4150	54
α-helix	4463-4468	6
α-helix	4472-4474	3
α-helix	4476-4505	30
α-helix	4509-4544	36
α-helix	4549-4551	3
β-strand	4552-4555	4	51
β-strand	4558-4562	5	51

Chain B: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	19-33	15
α-helix	45-53	9
β-strand	61-65	5	75
α-helix	66-75	10
β-strand	78	1	76
α-helix	85-88	4
α-helix	93-98	6
β-strand	100-101	2	77
β-strand	104-105	2	77
β-strand	108-113	6	75
β-strand	116-120	5	78
α-helix	127-128	2
β-strand	130	1	79
α-helix	134-143	10
α-helix	159-163	5
α-helix	164-166	3
β-strand	173	1	80
β-strand	178	1	80
α-helix	188-202	15
α-helix	212-219	8
β-strand	226-229	4	78
α-helix	231-239	9
β-strand	244-247	4	78
α-helix	248-250	3
β-strand	251-252	2	79
β-strand	255-256	2	79
β-strand	260	1	81
β-strand	262-268	7	75
β-strand	269	1	76
α-helix	275-278	4
α-helix	279-286	8
α-helix	289-298	10
α-helix	307-314	8
α-helix	317-328	12
β-strand	330	1	81
α-helix	331-333	3
α-helix	337-354	18
α-helix	359-370	12
α-helix	376-387	12
α-helix	393-407	15
α-helix	421-428	8
α-helix	436-448	13
α-helix	453-462	10
α-helix	464-469	6
β-strand	484-487	4	82
β-strand	496-499	4	82
α-helix	504-518	15
β-strand	523-527	5	83
β-strand	532-536	5	83

Chain H: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	61
β-strand	6-7	2	62
β-strand	10-12	3	63
β-strand	18-20	3	64
β-strand	21-22	2	62
β-strand	23	1	64
β-strand	25	1	61
β-strand	34-40	7	63
β-strand	44-51	8	63
β-strand	58-59	2	63
α-helix	62-64	3
β-strand	69-73	5	64
β-strand	78-83	6	64
α-helix	88-90	3
β-strand	92-96	5	63
β-strand	97	1	65
β-strand	113	1	65
β-strand	117-121	5	63
β-strand	130-134	5	66
β-strand	147-153	7	66
β-strand	163-164	2	67
β-strand	187-193	7	66
β-strand	206-210	5	67
β-strand	215-219	5	67

Chain I: 1 helix, 20 β-strands

Element	Residues	Length	Sheet
β-strand	401-403	3	84
β-strand	410-412	3	84
β-strand	429-431	3	85
β-strand	444-445	2	85
β-strand	497-501	5	86
α-helix	503-505	3
β-strand	508-513	6	86
β-strand	519	1	87
β-strand	525	1	88
β-strand	530	1	88
β-strand	535	1	87
β-strand	544-545	2	89
β-strand	552-553	2	89
β-strand	563-567	5	90
β-strand	575-579	5	90
β-strand	585-588	4	90
β-strand	597-598	2	90
β-strand	606	1	91
β-strand	612	1	91
β-strand	619-622	4	91
β-strand	627-630	4	91

Chain L: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	68
β-strand	13	1	69
β-strand	19-21	3	70
β-strand	24-25	2	68
β-strand	39	1	71
β-strand	40-43	4	72
β-strand	44	1	73
β-strand	51-55	5	72
β-strand	59-60	2	72
β-strand	68-71	4	70
β-strand	78-81	4	70
α-helix	86-88	3
β-strand	91	1	73
β-strand	96	1	71
β-strand	102	1	71
β-strand	108	1	73
β-strand	111	1	69
β-strand	119-123	5	74
α-helix	124-126	3
α-helix	127-131	5
β-strand	137-144	8	74
β-strand	164-166	3	74
β-strand	178-184	7	74

Chain N: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	92
β-strand	11-12	2	93
β-strand	17-26	10	92
β-strand	33-35	3	94
β-strand	37-39	3	95
α-helix	44-45	2
β-strand	46-47	2	95
β-strand	49	1	96
β-strand	51	1	94
β-strand	60	1	96
α-helix	62-64	3
β-strand	68-73	6	92
β-strand	78-84	7	92
β-strand	92-94	3	95
β-strand	97-99	3	94
β-strand	112	1	94
β-strand	117-119	3	95
β-strand	120-121	2	93

Chain R: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	72-74	3	97
β-strand	82-84	3	97
α-helix	85-87	3
β-strand	113-115	3	98
β-strand	121-123	3	98
α-helix	124-126	3
α-helix	138-141	4
β-strand	152-154	3	99
β-strand	160-162	3	99
α-helix	185-188	4
β-strand	203-204	2	100
β-strand	208-209	2	100
α-helix	212-214	3
β-strand	241-242	2	101
β-strand	248-249	2	101
α-helix	322-324	3
α-helix	339-341	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apolipoprotein B-100	A	protein	4563	Homo sapiens	P04114
Legobody 8D3 Fab Heavy Chain	H	protein	234	Mus musculus
Legobody 8D3 Fab Light Chain	L	protein	219	Mus musculus
Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G	B	protein	545	Escherichia coli, Staphylococcus aureus	P02976 (AlphaFold model), P06654 (AlphaFold model), P0AEX9 (AlphaFold model)
Low-density lipoprotein receptor	I, R	protein	860	Homo sapiens	P01130
ApoB100 nanobody 4	N	protein	131	Camelus bactrianus

Sequence of entity 1 (A), FASTA

>9BDT_1 Apolipoprotein B-100 (chains A)
MDPPRPALLALLALPALLLLLLAGARAEEEMLENVSLVCPKDATRFKHLRKYTYNYEAES
SSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCTLKEVYGFNPEGKALLKKTKNSE
EFAAAMSRYELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLFLD
TVYGNCSTHFTVKTRKGNVATEISTERDLGQCDRFKPIRTGISPLALIKGMTRPLSTLIS
SSQSCQYTLDAKRKHVAEAICKEQHLFLPFSYKNKYGMVAQVTQTLKLEDTPKINSRFFG
EGTKKMGLAFESTKSTSPPKQAEAVLKTLQELKKLTISEQNIQRANLFNKLVTELRGLSD
EAVTSLLPQLIEVSSPITLQALVQCGQPQCSTHILQWLKRVHANPLLIDVVTYLVALIPE
PSAQQLREIFNMARDQRSRATLYALSHAVNNYHKTNPTGTQELLDIANYLMEQIQDDCTG
DEDYTYLILRVIGNMGQTMEQLTPELKSSILKCVQSTKPSLMIQKAAIQALRKMEPKDKD
QEVLLQTFLDDASPGDKRLAAYLMLMRSPSQADINKIVQILPWEQNEQVKNFVASHIANI
LNSEELDIQDLKKLVKEALKESQLPTVMDFRKFSRNYQLYKSVSLPSLDPASAKIEGNLI
FDPNNYLPKESMLKTTLTAFGFASADLIEIGLEGKGFEPTLEALFGKQGFFPDSVNKALY
WVNGQVPDGVSKVLVDHFGYTKDDKHEQDMVNGIMLSVEKLIKDLKSKEVPEARAYLRIL
GEELGFASLHDLQLLGKLLLMGARTLQGIPQMIGEVIRKGSKNDFFLHYIFMENAFELPT
GAGLQLQISSSGVIAPGAKAGVKLEVANMQAELVAKPSVSVEFVTNMGIIIPDFARSGVQ
MNTNFFHESGLEAHVALKAGKLKFIIPSPKRPVKLLSGGNTLHLVSTTKTEVIPPLIENR
QSWSVCKQVFPGLNYCTSGAYSNASSTDSASYYPLTGDTRLELELRPTGEIEQYSVSATY
ELQREDRALVDTLKFVTQAEGAKQTEATMTFKYNRQSMTLSSEVQIPDFDVDLGTILRVN
DESTEGKTSYRLTLDIQNKKITEVALMGHLSCDTKEERKIKGVISIPRLQAEARSEILAH
WSPAKLLLQMDSSATAYGSTVSKRVAWHYDEEKIEFEWNTGTNVDTKKMTSNFPVDLSDY
PKSLHMYANRLLDHRVPQTDMTFRHVGSKLIVAMSSWLQKASGSLPYTQTLQDHLNSLKE
FNLQNMGLPDFHIPENLFLKSDGRVKYTLNKNSLKIEIPLPFGGKSSRDLKMLETVRTPA
LHFKSVGFHLPSREFQVPTFTIPKLYQLQVPLLGVLDLSTNVYSNLYNWSASYSGGNTST
DHFSLRARYHMKADSVVDLLSYNVQGSGETTYDHKNTFTLSCDGSLRHKFLDSNIKFSHV
EKLGNNPVSKGLLIFDASSSWGPQMSASVHLDSKKKQHLFVKEVKIDGQFRVSSFYAKGT
YGLSCQRDPNTGRLNGESNLRFNSSYLQGTNQITGRYEDGTLSLTSTSDLQSGIIKNTAS
LKYENYELTLKSDTNGKYKNFATSNKMDMTFSKQNALLRSEYQADYESLRFFSLLSGSLN
SHGLELNADILGTDKINSGAHKATLRIGQDGISTSATTNLKCSLLVLENELNAELGLSGA
SMKLTTNGRFREHNAKFSLDGKAALTELSLGSAYQAMILGVDSKNIFNFKVSQEGLKLSN
DMMGSYAEMKFDHTNSLNIAGLSLDFSSKLDNIYSSDKFYKQTVNLQLQPYSLVTTLNSD
LKYNALDLTNNGKLRLEPLKLHVAGNLKGAYQNNEIKHIYAISSAALSASYKADTVAKVQ
GVEFSHRLNTDIAGLASAIDMSTNYNSDSLHFSNVFRSVMAPFTMTIDAHTNGNGKLALW
GEHTGQLYSKFLLKAEPLAFTFSHDYKGSTSHHLVSRKSISAALEHKVSALLTPAEQTGT
WKLKTQFNNNEYSQDLDAYNTKDKIGVELTGRTLADLTLLDSPIKVPLLLSEPINIIDAL
EMRDAVEKPQEFTIVAFVKYDKNQDVHSINLPFFETLQEYFERNRQTIIVVLENVQRNLK
HINIDQFVRKYRAALGKLPQQANDYLNSFNWERQVSHAKEKLTALTKKYRITENDIQIAL
DDAKINFNEKLSQLQTYMIQFDQYIKDSYDLHDLKIAIANIIDEIIEKLKSLDEHYHIRV
NLVKTIHDLHLFIENIDFNKSGSSTASWIQNVDTKYQIRIQIQEKLQQLKRHIQNIDIQH
LAGKLKQHIEAIDVRVLLDQLGTTISFERINDILEHVKHFVINLIGDFEVAEKINAFRAK
VHELIERYEVDQQIQVLMDKLVELAHQYKLKETIQKLSNVLQQVKIKDYFEKLVGFIDDA
VKKLNELSFKTFIEDVNKFLDMLIKKLKSFDYHQFVDETNDKIREVTQRLNGEIQALELP
QKAEALKLFLEETKATVAVYLESLQDTKITLIINWLQEALSSASLAHMKAKFRETLEDTR
DRMYQMDIQQELQRYLSLVGQVYSTLVTYISDWWTLAAKNLTDFAEQYSIQDWAKRMKAL
VEQGFTVPEIKTILGTMPAFEVSLQALQKATFQTPDFIVPLTDLRIPSVQINFKDLKNIK
IPSRFSTPEFTILNTFHIPSFTIDFVEMKVKIIRTIDQMLNSELQWPVPDIYLRDLKVED
IPLARITLPDFRLPEIAIPEFIIPTLNLNDFQVPDLHIPEFQLPHISHTIEVPTFGKLYS
ILKIQSPLFTLDANADIGNGTTSANEAGIAASITAKGESKLEVLNFDFQANAQLSNPKIN
PLALKESVKFSSKYLRTEHGSEMLFFGNAIEGKSNTVASLHTEKNTLELSNGVIVKINNQ
LTLDSNTKYFHKLNIPKLDFSSQADLRNEIKTLLKAGHIAWTSSGKGSWKWACPRFSDEG
THESQISFTIEGPLTSFGLSNKINSKHLRVNQNLVYESGSLNFSKLEIQSQVDSQHVGHS
VLTAKGMALFGEGKAEFTGRHDAHLNGKVIGTLKNSLFFSAQPFEITASTNNEGNLKVRF
PLRLTGKIDFLNNYALFLSPSAQQASWQVSARFNQYKYNQNFSAGNNENIMEAHVGINGE
ANLDFLNIPLTIPEMRLPYTIITTPPLKDFSLWEKTGLKEFLKTTKQSFDLSVKAQYKKN
KHRHSITNPLAVLCEFISQSIKSFDRHFEKNRNNALDFVTKSYNETKIKFDKYKAEKSHD
ELPRTFQIPGYTVPVVNVEVSPFTIEMSAFGYVFPKAVSMPSFSILGSDVRVPSYTLILP
SLELPVLHVPRNLKLSLPDFKELCTISHIFIPAMGNITYDFSFKSSVITLNTNAELFNQS
DIVAHLLSSSSSVIDALQYKLEGTTRLTRKRGLKLATALSLSNKFVEGSHNSTVSLTTKN
MEVSVATTTKAQIPILRMNFKQELNGNTKSKPTVSSSMEFKYDFNSSMLYSTAKGAVDHK
LSLESLTSYFSIESSTKGDVKGSVLSREYSGTIASEANTYLNSKSTRSSVKLQGTSKIDD
IWNLEVKENFAGEATLQRIYSLWEHSTKNHLQLEGLFFTNGEHTSKATLELSPWQMSALV
QVHASQPSSFHDFPDLGQEVALNANTKNQKIRWKNEVRIHSGSFQSQVELSNDQEKAHLD
IAGSLEGHLRFLKNIILPVYDKSLWDFLKLDVTTSIGRRQHLRVSTAFVYTKNPNGYSFS
IPVKVLADKFIIPGLKLNDLNSVLVMPTFHVPFTDLQVPSCKLDFREIQIYKKLRTSSFA
LNLPTLPEVKFPEVDVLTKYSQPEDSLIPFFEITVPESQLTVSQFTLPKSVSDGIAALDL
NAVANKIADFELPTIIVPEQTIEIPSIKFSVPAGIVIPSFQALTARFEVDSPVYNATWSA
SLKNKADYVETVLDSTCSSTVQFLEYELNVLGTHKIEDGTLASKTKGTFAHRDFSAEYEE
DGKYEGLQEWEGKAHLNIKSPAFTDLHLRYQKDKKGISTSAASPAVGTVGMDMDEDDDFS
KWNFYYSPQSSPDKKLTIFKTELRVRESDEETQIKVNWEEEAASGLLTSLKDNVPKATGV
LYDYVNKYHWEHTGLTLREVSSKLRRNLQNNAEWVYQGAIRQIDDIDVRFQKAASGTTGT
YQEWKDKAQNLYQELLTQEGQASFQGLKDNVFDGLVRVTQEFHMKVKHLIDSLIDFLNFP
RFQFPGKPGIYTREELCTMFIREVGTVLSQVYSKVHNGSEILFSYFQDLVITLPFELRKH
KLIDVISMYRELLKDLSKEAQEVFKAIQSLKTTEVLRNLQDLLQFIFQLIEDNIKQLKEM
KFTYLINYIQDEINTIFSDYIPYVFKLLKENLCLNLHKFNEFIQNELQEASQELQQIHQY
IMALREEYFDPSIVGWTVKYYELEEKIVSLIKNLLVALKDFHSEYIVSASNFTSQLSSQV
EQFLHRNIQEYLSILTDPDGKGKEKIAELSATAQEIIKSQAIATKKIISDYHQQFRYKLQ
DFSDQLSDYYEKFIAESKRLIDLSIQNYHTFLIYITELLKKLQSTTVMNPYMKLAPGELT
IIL

Sequence of entity 2 (H), FASTA

>9BDT_2 Legobody 8D3 Fab Heavy Chain (chains H)
DVQLVESGGGLVQPGKSLRLSCAASGFTFSNFGMHWVRQAPEMGLEWVAYISSGSTTKYY
GDTVKGRFTISRDNPKNTLYLQMNSLRSEDTAMYYCARRPLYDGDYGYPMDYWGQGTSVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 3 (L), FASTA

>9BDT_3 Legobody 8D3 Fab Light Chain (chains L)
NIMLTQSPSSLAVSAGERVTMSCKSTQSILYNSNQKTYLAWYQQKPGQSPKLLIYWASTR
ASGVPDRFTGSGSGTDFTLTINSVQPEDLAVYYCHQYLSAWTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (B), FASTA

>9BDT_4 Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G (chains B)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDQ
ALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNEHQAPKGGSGGAGSGDQ
QSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAGGGSGGGSGGSAV
TTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEGSGH
HHHHH

Sequence of entity 5 (I, R), FASTA

>9BDT_5 Low-density lipoprotein receptor (chains I, R)
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQ
ETCLSVTCKSGDFSCGGRVNRCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGK
CISRQFVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEW
PQRCRGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDE
FQCSDGNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMAR
DCRDWSDEPIKECGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQD
PDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYT
SLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLA
VDWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPA
KIKKGGLNGVDIYSLVTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILE
DEKRLAHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHNLTQ
PRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA
TQETSTVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGN
EKKPSSVRALSIVLPIVLLVFLCLGVFLLWKNWRLKNINSINFDNPVYQKTTEDEVHICH
NQDGYSYPSRQMVSLEDDVA

Sequence of entity 6 (N), FASTA

>9BDT_6 ApoB100 nanobody 4 (chains N)
QVQLQESGGGLVQAGGSLRLSCVASGYTDGAVNMGWFRQAPGKDRDWVAAISPGGGLTYY
ADSVKGRFTISQDKAKNTVYLQMNSLKPEDTAIYYCAAARSLAHFKLSQYNYWGQGTQVT
VSSLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor. Reimund, M., Dearborn, A.D., Graziano, G. et al. Nature (2025) 638:829-835. DOI 10.1038/s41586-024-08223-0 · PubMed

Other PDB entries of the same protein (UniProt P04114), best resolution first:

9COO 3.73 Å, Nanobody 4 bound to Apolipoprotein B 100
9BDE 4.18 Å, Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor
9BD8 4.8 Å, ApoB 100 beta barrel bound to LDLR beta propeller
9BD1 5.4 Å, beta/alpha1 region of ApoB 100
9E9R 9.0 Å, The Structure of ApoB100 from Human Low-Density Lipoprotein
9EA7 9.0 Å, The Structure of ApoB100 from Human Low-Density Lipoprotein
9EAG 9.0 Å, The Structure of ApoB100 from Human Low-Density Lipoprotein

Browse structure collections

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