9E9R: ApoB100 from Human Low-Density Lipoprotein

The Structure of ApoB100 from Human Low-Density Lipoprotein. Determined by electron microscopy at 9.0 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 9.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 29,417
Mol. weight: 516.17 kDa
Released: 18 Dec 2024

Explore 9E9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E9R contains 83 α-helices and 216 β-strands across 1 chain. 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: 83 helices, 216 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
β-strand	50-64	15	1
α-helix	65-67	3
β-strand	70-86	17	1
β-strand	89-105	17	1
β-strand	111-115	5	1
α-helix	119-127	9
β-strand	130-134	5	1
α-helix	136-138	3
β-strand	142-144	3	1
α-helix	151-164	14
α-helix	167-169	3
β-strand	176-181	6	1
β-strand	184-196	13	1
β-strand	199-208	10	1
α-helix	213-215	3
α-helix	217	1
β-strand	218	1	2
α-helix	219	1
α-helix	232-237	6
β-strand	239-249	11	1
β-strand	256-267	12	1
α-helix	272-274	3
β-strand	278-290	13	1
β-strand	293	1	1
β-strand	306-307	2	1
α-helix	321-338	18
α-helix	344-357	14
α-helix	360-373	14
α-helix	375-384	10
α-helix	388-400	13
α-helix	405-416	12
α-helix	423-436	14
α-helix	439-455	17
α-helix	461-474	14
α-helix	482-493	12
α-helix	496-502	7
α-helix	504-515	12
α-helix	521-530	10
α-helix	531-533	3
α-helix	538-549	12
α-helix	555-565	11
α-helix	571-580	10
α-helix	581-583	3
α-helix	587-602	16
α-helix	606-618	13
α-helix	624-626	3
β-strand	635-643	9	3
α-helix	649-650	2
β-strand	651-659	9	3
β-strand	660	1	4
β-strand	670	1	4
β-strand	671-680	10	3
β-strand	683-695	13	3
α-helix	697-705	9
α-helix	710-721	12
α-helix	728-738	11
α-helix	749-766	18
α-helix	769-771	3
β-strand	772-779	8	3
β-strand	782-788	7	3
α-helix	789-819	31
β-strand	823-825	3	5
β-strand	829-839	11	2
β-strand	845-854	10	2
β-strand	858-860	3	5
β-strand	863-865	3	6
β-strand	870-875	6	6
β-strand	876-877	2	5
β-strand	878-891	14	2
β-strand	895-908	14	2
β-strand	911-918	8	6
β-strand	921-927	7	6
α-helix	928-929	2
β-strand	933-941	9	2
β-strand	943-946	4	2
β-strand	949-952	4	2
α-helix	954-956	3
β-strand	960-968	9	2
β-strand	973-982	10	2
β-strand	999-1007	9	2
β-strand	1011-1025	15	6
β-strand	1028-1041	14	6
β-strand	1047-1054	8	6
β-strand	1059-1065	7	6
β-strand	1066	1	7
α-helix	1067-1069	3
β-strand	1071	1	7
β-strand	1074-1081	8	6
β-strand	1087-1098	12	6
β-strand	1101-1113	13	6
β-strand	1118-1126	9	6
β-strand	1131-1140	10	6
β-strand	1147-1156	10	6
β-strand	1159-1169	11	6
β-strand	1174-1185	12	6
α-helix	1186-1192	7
α-helix	1200-1213	14
α-helix	1223-1240	18
α-helix	1246-1259	14
β-strand	1276-1287	12	6
β-strand	1293-1297	5	8
β-strand	1347-1351	5	8
α-helix	1354-1355	2
β-strand	1356-1364	9	6
β-strand	1367-1375	9	6
β-strand	1379	1	6
β-strand	1384-1385	2	6
β-strand	1388-1395	8	6
β-strand	1402-1407	6	6
β-strand	1410-1413	4	6
β-strand	1417-1427	11	6
β-strand	1431-1442	12	6
β-strand	1449-1459	11	6
β-strand	1464-1476	13	6
β-strand	1479-1491	13	6
β-strand	1496-1508	13	6
β-strand	1513-1524	12	6
β-strand	1528-1538	11	6
β-strand	1541-1550	10	6
β-strand	1555-1564	10	6
β-strand	1567-1576	10	6
β-strand	1578	1	9
β-strand	1581	1	9
β-strand	1584-1591	8	6
β-strand	1596-1603	8	6
β-strand	1606	1	9
β-strand	1609	1	9
β-strand	1610-1619	10	6
β-strand	1624-1633	10	6
β-strand	1638-1648	11	6
β-strand	1651-1662	12	6
β-strand	1665-1676	12	6
β-strand	1680-1686	7	6
β-strand	1689-1690	2	6
β-strand	1693-1703	11	6
β-strand	1708-1716	9	6
α-helix	1718-1720	3
β-strand	1722-1731	10	6
β-strand	1737-1746	10	6
β-strand	1749-1760	12	6
β-strand	1763-1775	13	6
β-strand	1778-1789	12	6
β-strand	1792-1803	12	6
β-strand	1806-1817	12	6
β-strand	1820-1831	12	6
β-strand	1834-1845	12	6
β-strand	1848-1859	12	6
β-strand	1862-1868	7	6
β-strand	1878-1886	9	6
β-strand	1890-1899	10	6
β-strand	1905-1917	13	6
β-strand	1922-1936	15	6
β-strand	1939-1954	16	6
β-strand	1958-1972	15	6
β-strand	1976-1987	12	6
β-strand	1990-2001	12	6
β-strand	2004-2015	12	6
α-helix	2018-2021	4
α-helix	2036-2040	5
β-strand	2050-2062	13	6
α-helix	2066	1
β-strand	2067-2069	3	10
α-helix	2072-2100	29
α-helix	2387-2406	20
α-helix	2409-2428	20
α-helix	2432-2455	24
α-helix	2739-2741	3
β-strand	2750-2752	3	10
β-strand	2755-2765	11	6
β-strand	2770-2779	10	6
β-strand	2786-2795	10	6
β-strand	2797-2798	2	6
α-helix	2802-2804	3
β-strand	2808-2817	10	6
β-strand	2821-2832	12	6
β-strand	2835-2846	12	6
β-strand	2849-2861	13	6
β-strand	2865-2877	13	6
β-strand	2881-2895	15	6
β-strand	2900-2915	16	6
β-strand	2918-2932	15	6
β-strand	2937-2951	15	6
β-strand	2954-2965	12	6
β-strand	2968-2979	12	6
β-strand	2983-2994	12	6
β-strand	2998-3009	12	6
β-strand	3014-3025	12	6
β-strand	3029-3042	14	6
β-strand	3045-3060	16	6
β-strand	3064-3078	15	6
β-strand	3083-3093	11	6
β-strand	3096-3106	11	6
β-strand	3111	1	6
β-strand	3114-3121	8	6
α-helix	3124-3127	4
β-strand	3130-3132	3	11
β-strand	3135-3136	2	12
α-helix	3137	1
β-strand	3143-3144	2	12
α-helix	3145-3146	2
β-strand	3147-3150	4	11
α-helix	3152-3155	4
α-helix	3158-3162	5
β-strand	3167-3174	8	6
β-strand	3177	1	6
β-strand	3183-3187	5	13
α-helix	3188	1
α-helix	3191-3194	4
β-strand	3328-3332	5	13
β-strand	3337-3344	8	6
β-strand	3348-3357	10	6
β-strand	3362-3372	11	6
β-strand	3379-3388	10	6
β-strand	3390	1	14
β-strand	3392	1	14
β-strand	3394-3402	9	6
β-strand	3406-3416	11	6
β-strand	3421-3432	12	6
β-strand	3436-3448	13	6
β-strand	3452-3466	15	6
β-strand	3471-3485	15	6
β-strand	3490-3504	15	6
β-strand	3507-3521	15	6
β-strand	3525-3533	9	6
β-strand	3536-3538	3	6
β-strand	3541	1	6
β-strand	3545-3546	2	15
β-strand	3550-3555	6	6
β-strand	3559-3562	4	6
β-strand	3567-3568	2	15
β-strand	3570-3571	2	16
β-strand	3579-3580	2	16
β-strand	3583	1	17
α-helix	3584-3586	3
β-strand	3587-3592	6	6
β-strand	3595-3602	8	6
β-strand	3604	1	17
β-strand	3615-3625	11	6
β-strand	3628-3639	12	6
β-strand	3642-3652	11	6
β-strand	3656-3668	13	6
α-helix	3670-3673	4
β-strand	3676-3677	2	18
β-strand	3682-3683	2	18
α-helix	3684-3688	5
β-strand	3699-3711	13	6
β-strand	3717-3720	4	19
β-strand	3724-3725	2	20
β-strand	3729-3732	4	20
β-strand	3743-3746	4	21
β-strand	3750	1	22
α-helix	3756	1
β-strand	3757	1	22
α-helix	3758-3760	3
β-strand	3761-3764	4	21
β-strand	3768-3771	4	20
β-strand	3773-3776	4	23
β-strand	3779-3780	2	24
β-strand	3789-3791	3	24
β-strand	3794-3801	8	23
β-strand	3810-3815	6	23
β-strand	3818-3822	5	24
β-strand	3825-3827	3	25
β-strand	3831-3832	2	26
β-strand	3837-3838	2	26
α-helix	3840-3848	9
α-helix	3852-3854	3
β-strand	3855-3857	3	25
β-strand	3860-3864	5	24
β-strand	3867-3872	6	23
β-strand	3874-3877	4	19
α-helix	3878-3880	3
β-strand	3882-3890	9	6
β-strand	3895-3905	11	6
β-strand	3908-3918	11	6
α-helix	3922-3924	3
β-strand	3926-3937	12	6
β-strand	3940-3951	12	6
β-strand	3954-3965	12	6
β-strand	3969-3979	11	6
β-strand	3986-3993	8	6
β-strand	3996-4003	8	6
β-strand	4007-4015	9	6
β-strand	4019-4028	10	6
β-strand	4036-4045	10	6
β-strand	4052-4058	7	6
α-helix	4060-4093	34
α-helix	4097-4160	64
α-helix	4165-4198	34
α-helix	4293-4319	27
α-helix	4323-4387	65
α-helix	4395-4437	43
α-helix	4439-4455	17
α-helix	4457-4458	2
α-helix	4461-4507	47
α-helix	4509-4543	35
β-strand	4552-4555	4	6
β-strand	4558-4562	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apolipoprotein B 100	A	protein	4563	Homo sapiens	P04114

Sequence of entity 1 (A), FASTA

>9E9R_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

Primary citation

The structure of apolipoprotein B100 from human low-density lipoprotein. Berndsen, Z.T., Cassidy, C.K. Nature (2025) 638:836-843. DOI 10.1038/s41586-024-08467-w · 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
9BDT 5.4 Å, Apolipoprotein B 100 bound to LDL receptor and legobody
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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