7NOZ: Complement C3 beta chain

Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP. Determined by X-ray diffraction at 3.9 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 3.9 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 21,994
Mol. weight: 317.06 kDa
Ligands: MG, NAG, MAN
Released: 27 Jul 2022

Explore 7NOZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NOZ contains 82 α-helices and 202 β-strands across 6 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: 13 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	33-35	3	2
β-strand	39-47	9	1
β-strand	53-61	9	2
β-strand	68-76	9	2
α-helix	78-80	3
β-strand	83-89	7	1
β-strand	104-112	9	2
β-strand	115-124	10	2
β-strand	129-134	6	3
β-strand	138-139	2	4
β-strand	144-152	9	3
β-strand	158	1	3
β-strand	162-168	7	4
β-strand	174-181	8	4
β-strand	188-194	7	3
α-helix	195-196	2
β-strand	202-210	9	4
β-strand	218-224	7	4
β-strand	232-238	7	5
β-strand	243-244	2	6
β-strand	251-259	9	5
β-strand	264	1	5
β-strand	267-277	11	7
β-strand	280-283	4	7
α-helix	285-287	3
β-strand	289-293	5	7
β-strand	294	1	5
β-strand	297-302	6	5
α-helix	304-311	8
α-helix	317-319	3
β-strand	320	1	8
β-strand	322	1	8
β-strand	323-332	10	7
β-strand	338-347	10	7
β-strand	348-349	2	6
β-strand	354-356	3	9
β-strand	363-364	2	10
β-strand	370-377	8	9
β-strand	383	1	9
β-strand	388-391	4	11
β-strand	398-400	3	11
α-helix	401	1
β-strand	406-411	6	9
β-strand	420-426	7	11
α-helix	433-435	3
β-strand	438-443	6	11
β-strand	444-445	2	10
α-helix	446-448	3
β-strand	455-460	6	12
β-strand	465	1	13
β-strand	470-478	9	12
α-helix	484-486	3
β-strand	489-496	8	14
β-strand	499-507	9	14
β-strand	514-520	7	12
α-helix	523-525	3
β-strand	528-538	11	14
β-strand	544-554	11	14
β-strand	555	1	13
β-strand	563-567	5	15
α-helix	574-576	3
β-strand	580-587	8	15
β-strand	592-599	8	16
α-helix	613-621	9
α-helix	635-642	8
β-strand	644-648	5	1
β-strand	653	1	1

Chain B: 33 helices, 53 β-strands

Element	Residues	Length	Sheet
α-helix	758-760	3
α-helix	761-763	3
β-strand	764	1	17
β-strand	770-771	2	16
β-strand	775-777	3	16
β-strand	783	1	18
β-strand	786	1	18
β-strand	787-794	8	15
β-strand	801-810	10	16
β-strand	814-817	4	16
α-helix	818-820	3
β-strand	821-824	4	16
β-strand	829-834	6	19
β-strand	838-840	3	17
β-strand	845-853	9	19
β-strand	860-866	7	17
α-helix	867-868	2
β-strand	872	1	20
β-strand	882-888	7	17
β-strand	892-900	9	19
β-strand	902	1	20
β-strand	906-916	11	17
β-strand	922-932	11	17
α-helix	933	1
β-strand	936-947	12	21
β-strand	954	1	22
β-strand	957-962	6	22
β-strand	970	1	21
α-helix	971	1
β-strand	977-984	8	21
α-helix	993-996	4
α-helix	997-1003	7
α-helix	1013-1031	19
α-helix	1034-1037	4
α-helix	1042-1057	16
β-strand	1060	1	23
β-strand	1066	1	23
α-helix	1073-1074	2
α-helix	1076-1088	13
α-helix	1097-1109	13
α-helix	1131-1133	3
α-helix	1139-1152	14
α-helix	1165-1178	14
α-helix	1179-1182	4
α-helix	1186-1197	12
α-helix	1205-1211	7
β-strand	1215	1	24
β-strand	1219	1	24
α-helix	1226-1242	17
α-helix	1249-1258	10
α-helix	1269-1285	17
β-strand	1293-1299	7	22
β-strand	1307-1311	5	22
β-strand	1322-1324	3	21
β-strand	1330-1337	8	22
β-strand	1340-1350	11	21
β-strand	1361-1369	9	25
β-strand	1383-1392	10	25
β-strand	1398	1	26
β-strand	1401-1406	6	27
α-helix	1407-1408	2
β-strand	1412-1413	2	25
α-helix	1415-1422	8
β-strand	1427-1428	2	27
α-helix	1431-1434	4
β-strand	1443-1448	6	27
β-strand	1451	1	26
β-strand	1457-1464	8	25
α-helix	1473-1474	2
β-strand	1475-1481	7	27
β-strand	1489-1493	5	27
α-helix	1498-1500	3
α-helix	1501-1503	3
β-strand	1504-1507	4	28
β-strand	1510-1513	4	28
α-helix	1529-1536	8
β-strand	1541-1555	15	29
β-strand	1558-1570	13	29
β-strand	1581-1586	6	29
α-helix	1591-1594	4
β-strand	1601-1607	7	29
β-strand	1611	1	29
β-strand	1619-1621	3	29
β-strand	1626-1631	6	29
α-helix	1636-1638	3
α-helix	1643-1657	15

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	30
β-strand	42-48	7	30
α-helix	53-56	4
β-strand	63-65	3	30
β-strand	72-74	3	30
β-strand	79-80	2	31
α-helix	82-89	8
β-strand	98-103	6	32
β-strand	104-105	2	31
β-strand	111	1	33
β-strand	115	1	33
β-strand	120-125	6	32
α-helix	141-148	8
β-strand	154-160	7	34
α-helix	167-168	2
β-strand	179-185	7	34

Chain D: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	265-268	4
β-strand	275-279	5	35
β-strand	303-307	5	35
α-helix	311-313	3
β-strand	314	1	36
β-strand	317-318	2	37
α-helix	323-326	4
β-strand	328	1	38
β-strand	336	1	38
β-strand	342-347	6	38
β-strand	350-351	2	37
β-strand	354	1	36
α-helix	357-360	4
β-strand	365-372	8	38
β-strand	377-379	3	39
β-strand	380-382	3	40
α-helix	385-388	4
β-strand	392	1	41
β-strand	400-406	7	41
β-strand	407-409	3	40
β-strand	417-418	2	42
β-strand	427-428	2	42
β-strand	429-432	4	38
β-strand	436-438	3	39
β-strand	448-454	7	41
α-helix	458-460	3

Chain F: 25 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	44-45	2	43
β-strand	48-52	5	44
β-strand	57-61	5	44
β-strand	66-68	3	45
β-strand	73-75	3	44
β-strand	85-86	2	46
β-strand	92-93	2	46
β-strand	96-97	2	43
β-strand	98-100	3	45
α-helix	101	1
β-strand	103	1	47
α-helix	104-105	2
β-strand	112-115	4	48
β-strand	121	1	47
β-strand	126-131	6	48
β-strand	136-138	3	49
β-strand	142-144	3	48
β-strand	145	1	50
β-strand	151	1	50
α-helix	155-156	2
β-strand	157-159	3	49
α-helix	166-167	2
β-strand	175-177	3	51
β-strand	186-190	5	51
β-strand	196-198	3	52
β-strand	202-204	3	51
β-strand	205-206	2	53
β-strand	210-211	2	53
β-strand	217-219	3	52
α-helix	227-238	12
α-helix	240-243	4
β-strand	269-276	8	54
α-helix	287-301	15
β-strand	308-314	7	54
β-strand	318-322	5	54
α-helix	332-341	10
α-helix	345-349	5
α-helix	355-366	12
β-strand	381-388	8	54
α-helix	399-408	10
α-helix	420-422	3
β-strand	423-429	7	54
α-helix	436-442	7
β-strand	452-454	3	54
α-helix	459-470	12
α-helix	472-473	2
β-strand	496-503	8	55
β-strand	507-515	9	55
β-strand	520-523	4	55
α-helix	534-536	3
β-strand	537-541	5	55
β-strand	548	1	55
β-strand	550-555	6	55
β-strand	578-582	5	55
α-helix	585-588	4
β-strand	596	1	56
β-strand	600	1	57
α-helix	601-606	6
α-helix	615-622	8
β-strand	627-635	9	56
β-strand	640-648	9	56
α-helix	653-657	5
α-helix	658-662	5
α-helix	672-674	3
β-strand	680-683	4	56
α-helix	691-694	4
β-strand	702-707	6	56
β-strand	710-720	11	56
β-strand	725	1	58
β-strand	730	1	58
β-strand	740-744	5	56
α-helix	749-755	7
β-strand	763	1	57

Chain R: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	59
β-strand	12-14	3	60
β-strand	19-25	7	59
β-strand	33-40	8	61
β-strand	47-52	6	61
β-strand	59-61	3	61
β-strand	66	1	59
β-strand	69-74	6	59
β-strand	79-84	6	59
α-helix	89-91	3
β-strand	93-101	9	61
β-strand	114-115	2	61
β-strand	119-121	3	61
β-strand	122-124	3	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3 beta chain	A	protein	645	Homo sapiens	P01024 (AlphaFold model)
Complement C3 alpha chain	B	protein	912	Homo sapiens	P01024 (AlphaFold model)
Properdin	C	protein	163	Homo sapiens	P27918 (AlphaFold model)
Properdin	D	protein	207	Homo sapiens	P27918 (AlphaFold model)
Complement factor B	F	protein	731	Homo sapiens	P00751 (AlphaFold model)
hFPNb1 nanobody	R	protein	124	Lama glama

Sequence of entity 1 (A), FASTA

>7NOZ_1 Complement C3 beta chain (chains A)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 2 (B), FASTA

>7NOZ_2 Complement C3 alpha chain (chains B)
DEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVSMSD
KKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLHNPA
FCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKSLKV
VPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVAQMT
EDAVDAERLKHLIVTPSGCGEENMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKK
GYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEK
QKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITK
AGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVE
ATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQE
LNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMYHAK
AKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMMTGF
APDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFNVEL
IQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVTLEE
RLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPIKCR
EALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQDLGA
FTESMVVFGCPN

Sequence of entity 3 (C), FASTA

>7NOZ_3 Properdin (chains C)
DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWA
PCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQCCPEMGGWSGWGPWEP
CSVTCSKGTRTRRRACNHPAPKCGGHCPGQAQESEACDTQQVC

Sequence of entity 4 (D), FASTA

>7NOZ_4 Properdin (chains D)
GVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPV
DGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQ
HCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGR
PLPRCEELQGQKLVVEEKRPCLHVPAC

Sequence of entity 5 (F), FASTA

>7NOZ_5 Complement factor B (chains F)
GSCSLEGVEIKGGSFRLLQEGQALEYVCPSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVR
KAECRAIHCPRPHDFENGEYWPRSPYYNVSDEISFHCYDGYTLRGSANRTCQVNGRWSGQ
TAICDNGAGYCSNPGIPIGTRKVGSQYRLEDSVTYHCSRGLTLRGSQRRTCQEGGSWSGT
EPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAEDGHGPGEQQKRKIVLDPSGSMNIYLV
LDGSGSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVSEADSSNADW
VTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNM
GGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKKDNEQHVFK
VKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGA
VVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYD
YDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVS
EEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNT
CRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKE
KLQDEDLGFLA

Sequence of entity 6 (R), FASTA

>7NOZ_6 hFPNb1 nanobody (chains R)
QVQLVESGGGLVQAGGSLRLSCAASERTFTIYAMGWFRQAPGKEREFVAAISRSGENTDY
ADSVKGRFTISRDNNKNTISLQMNSLKPEDTAVYYCAAGRAILVHTTKKEYDHWGQGTQV
TVSS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
MAN	alpha-D-mannopyranose	C6 H12 O6	6

Primary citation

Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging. Lorentzen, J., Pedersen, D.V., Gadeberg, T.A.F. et al. Protein Sci (2022) 31:e4432-e4432. DOI 10.1002/pro.4432 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
7UE9 1.75 Å, Structure of anti-C3d Fab(3d8b) in complex with C3d
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex

Browse structure collections

About this viewer

MolViewer shows 7NOZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.