9U62: AP pathways C3 convertase C3bBbP and C3 complex

AP pathways C3 convertase C3bBbP and C3 complex. Determined by electron microscopy at 2.7 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 29,513
Mol. weight: 670.36 kDa
Ligands: NI, NAG
Released: 14 Jan 2026

Explore 9U62 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U62 contains 119 α-helices and 255 β-strands across 5 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 B: 19 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	19
β-strand	268-275	8	20
α-helix	283-301	19
β-strand	308-313	6	20
β-strand	319-322	4	20
α-helix	327-329	3
α-helix	332-340	9
α-helix	344-347	4
α-helix	355-365	11
β-strand	380-388	9	20
α-helix	399-408	10
α-helix	420-422	3
β-strand	423-429	7	20
α-helix	436-440	5
β-strand	452-453	2	20
α-helix	461-466	6
β-strand	469-470	2	19
α-helix	489-492	4
β-strand	496-503	8	2
β-strand	507-515	9	2
β-strand	520-523	4	2
α-helix	534-536	3
β-strand	537-541	5	2
β-strand	548-555	8	2
β-strand	578-582	5	2
α-helix	585-588	4
β-strand	596	1	1
α-helix	597	1
β-strand	600	1	21
α-helix	601-606	6
α-helix	615-622	8
β-strand	627-636	10	1
β-strand	639-648	10	1
α-helix	653-658	6
α-helix	659-662	4
β-strand	680-684	5	1
α-helix	701	1
β-strand	702-707	6	1
β-strand	710-720	11	1
β-strand	726	1	22
β-strand	729	1	22
β-strand	739-744	6	1
α-helix	749-755	7
β-strand	763	1	21

Chain C: 14 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	58
β-strand	31	1	59
β-strand	33-36	4	60
β-strand	39-47	9	58
β-strand	53-62	10	60
β-strand	68-76	9	60
α-helix	78-80	3
β-strand	83-89	7	58
β-strand	105-112	8	60
β-strand	115-125	11	60
β-strand	129-134	6	61
β-strand	138-139	2	62
β-strand	144-152	9	61
β-strand	158	1	61
β-strand	162-168	7	62
β-strand	174-181	8	62
β-strand	188-194	7	61
α-helix	195-196	2
β-strand	202-210	9	62
β-strand	218-224	7	62
β-strand	233-238	6	63
β-strand	243-244	2	64
β-strand	251-258	8	63
β-strand	264	1	63
β-strand	267-277	11	65
β-strand	280-293	14	65
β-strand	298-302	5	63
α-helix	304-309	6
α-helix	316-319	4
β-strand	323-332	10	65
β-strand	338-347	10	65
β-strand	348-349	2	64
β-strand	354-357	4	66
β-strand	363-364	2	67
β-strand	369-377	9	66
β-strand	383	1	66
β-strand	388-391	4	68
β-strand	399-400	2	68
β-strand	406-412	7	66
β-strand	420-426	7	68
β-strand	438-443	6	68
β-strand	444-445	2	67
α-helix	446-448	3
α-helix	449-451	3
β-strand	455-459	5	69
α-helix	464	1
β-strand	465	1	70
β-strand	470-478	9	69
α-helix	484-486	3
β-strand	489-496	8	71
β-strand	499-507	9	71
β-strand	514-520	7	69
α-helix	523-525	3
β-strand	528-538	11	71
α-helix	540-542	3
β-strand	544-554	11	71
β-strand	555	1	70
β-strand	563-567	5	5
β-strand	580-587	8	5
β-strand	592-599	8	3
α-helix	600-604	5
α-helix	613-621	9
α-helix	635-641	7
β-strand	644	1	59
β-strand	647-648	2	58
β-strand	653	1	58
α-helix	654-657	4

Chain D: 41 helices, 57 β-strands

Element	Residues	Length	Sheet
α-helix	676-683	8
α-helix	688-690	3
α-helix	692-698	7
α-helix	700-701	2
α-helix	709-713	5
α-helix	718-742	25
β-strand	747	1	1
β-strand	750-752	3	2
α-helix	760-764	5
α-helix	768-770	3
β-strand	771	1	3
β-strand	775-777	3	3
α-helix	781-782	2
β-strand	783	1	4
β-strand	786	1	4
β-strand	787-794	8	5
β-strand	801-810	10	3
β-strand	814-817	4	3
α-helix	818-820	3
β-strand	821-824	4	3
β-strand	829-834	6	6
β-strand	839-840	2	7
β-strand	844-853	10	6
β-strand	860-866	7	7
α-helix	867-868	2
β-strand	872-873	2	8
β-strand	882-888	7	7
β-strand	892-900	9	6
β-strand	901-902	2	8
β-strand	906-916	11	7
β-strand	922-932	11	7
β-strand	936-947	12	9
α-helix	949-952	4
β-strand	954	1	10
β-strand	957-962	6	10
α-helix	963-965	3
β-strand	970	1	9
α-helix	971	1
β-strand	977-983	7	9
α-helix	988-995	8
α-helix	1001-1003	3
α-helix	1013-1016	4
α-helix	1019-1031	13
α-helix	1034-1037	4
α-helix	1039-1041	3
α-helix	1042-1056	15
α-helix	1057-1059	3
β-strand	1060	1	11
β-strand	1066	1	11
β-strand	1067	1	12
β-strand	1074	1	12
α-helix	1076-1088	13
α-helix	1097-1111	15
β-strand	1112	1	13
β-strand	1118	1	13
α-helix	1127-1129	3
α-helix	1137-1151	15
α-helix	1165-1178	14
α-helix	1180-1182	3
α-helix	1186-1199	14
α-helix	1205-1212	8
β-strand	1215	1	14
β-strand	1219	1	14
α-helix	1227-1242	16
α-helix	1249-1256	8
β-strand	1262	1	15
β-strand	1265	1	15
α-helix	1269-1282	14
β-strand	1294-1299	6	10
α-helix	1306	1
β-strand	1307-1311	5	10
β-strand	1319-1324	6	9
β-strand	1330-1336	7	10
β-strand	1340-1350	11	9
β-strand	1361-1369	9	16
α-helix	1370-1371	2
β-strand	1382-1392	11	16
β-strand	1401-1406	6	17
β-strand	1411-1413	3	16
α-helix	1415-1423	9
β-strand	1431-1434	4	17
β-strand	1443-1448	6	17
β-strand	1457-1465	9	16
β-strand	1468-1470	3	6
β-strand	1475-1481	7	17
β-strand	1484-1493	10	17
α-helix	1510-1514	5
α-helix	1529-1535	7
β-strand	1542-1553	12	18
β-strand	1558-1570	13	18
β-strand	1581-1587	7	18
α-helix	1588-1590	3
β-strand	1601-1606	6	18
α-helix	1608-1610	3
β-strand	1611-1613	3	18
β-strand	1618-1621	4	18
β-strand	1627-1630	4	18
α-helix	1645-1648	4

Chain E: 43 helices, 102 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	31
β-strand	33-35	3	32
β-strand	39-47	9	31
β-strand	53-61	9	32
β-strand	68-76	9	32
α-helix	78-80	3
β-strand	83-89	7	31
α-helix	90-92	3
β-strand	105-112	8	32
β-strand	115-124	10	32
β-strand	129-134	6	33
β-strand	138-139	2	34
β-strand	144-152	9	33
β-strand	158	1	33
β-strand	162-168	7	34
β-strand	174-181	8	34
β-strand	188-194	7	33
β-strand	202-210	9	34
β-strand	218-224	7	34
β-strand	232-238	7	35
β-strand	243-244	2	36
β-strand	251-259	9	35
β-strand	264	1	35
β-strand	267-277	11	37
β-strand	280-293	14	37
β-strand	298-302	5	35
α-helix	304-310	7
α-helix	316-319	4
β-strand	323-332	10	37
β-strand	338-347	10	37
β-strand	348-349	2	36
β-strand	354-356	3	38
β-strand	363-364	2	39
β-strand	369-377	9	38
β-strand	383	1	38
β-strand	388-391	4	40
β-strand	398-400	3	40
β-strand	406-412	7	38
α-helix	413-414	2
β-strand	420-426	7	40
α-helix	433-435	3
β-strand	438-443	6	40
β-strand	444-445	2	39
α-helix	446-447	2
β-strand	455-460	6	41
β-strand	465	1	42
β-strand	469-478	10	41
α-helix	484-486	3
β-strand	489-496	8	43
β-strand	499-507	9	43
β-strand	514-521	8	41
α-helix	523-525	3
β-strand	528-538	11	43
β-strand	544-554	11	43
β-strand	555	1	42
β-strand	563-567	5	44
α-helix	574-576	3
β-strand	580-587	8	44
β-strand	592-599	8	45
α-helix	602-605	4
α-helix	613-621	9
β-strand	630	1	43
α-helix	635-642	8
β-strand	644-648	5	31
β-strand	653	1	31
α-helix	654-657	4
α-helix	758-760	3
α-helix	761-763	3
β-strand	764	1	46
β-strand	770-771	2	45
β-strand	775-777	3	45
α-helix	781-782	2
β-strand	783	1	47
β-strand	786	1	47
β-strand	787-794	8	44
β-strand	801-810	10	45
β-strand	814-817	4	45
α-helix	818-820	3
β-strand	821-824	4	45
β-strand	829-834	6	48
β-strand	838-840	3	46
β-strand	845-853	9	48
β-strand	860-866	7	46
α-helix	867-868	2
β-strand	872-873	2	49
β-strand	882-888	7	46
β-strand	892-900	9	48
β-strand	901-902	2	49
β-strand	906-916	11	46
β-strand	922-932	11	46
β-strand	936-946	11	50
β-strand	958-962	5	51
α-helix	963-965	3
β-strand	970	1	50
β-strand	977-984	8	50
β-strand	988	1	52
α-helix	990-996	7
α-helix	997-1000	4
α-helix	1014-1031	18
α-helix	1034-1037	4
α-helix	1042-1051	10
α-helix	1077-1084	8
α-helix	1131-1134	4
α-helix	1139-1153	15
α-helix	1155-1158	4
α-helix	1171-1179	9
α-helix	1180-1182	3
α-helix	1189-1199	11
α-helix	1205-1213	9
β-strand	1215	1	53
β-strand	1219	1	53
α-helix	1227-1242	16
α-helix	1249-1259	11
α-helix	1271-1283	13
β-strand	1289	1	52
β-strand	1293-1297	5	51
β-strand	1309-1311	3	51
β-strand	1319-1324	6	50
β-strand	1330-1336	7	51
β-strand	1340-1350	11	50
β-strand	1361-1369	9	54
β-strand	1383-1392	10	54
β-strand	1401-1406	6	55
β-strand	1411-1413	3	54
α-helix	1415-1423	9
β-strand	1427-1428	2	55
α-helix	1431-1434	4
β-strand	1443-1448	6	55
β-strand	1457-1465	9	54
α-helix	1472-1474	3
β-strand	1475-1481	7	55
β-strand	1488-1493	6	55
α-helix	1501-1503	3
β-strand	1504-1507	4	56
β-strand	1510-1513	4	56
β-strand	1544-1553	10	57
β-strand	1558-1569	12	57
β-strand	1581-1587	7	57
β-strand	1601-1605	5	57
β-strand	1611-1613	3	57
β-strand	1618-1621	4	57
β-strand	1627-1631	5	57
α-helix	1632-1633	2
α-helix	1640-1642	3
α-helix	1643-1658	16

Chain P: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	314	1	23
β-strand	317-318	2	24
α-helix	324-327	4
β-strand	328	1	25
β-strand	329	1	26
β-strand	332	1	26
β-strand	342-347	6	25
β-strand	350-351	2	24
β-strand	354	1	23
β-strand	365-372	8	25
β-strand	382-385	4	27
β-strand	402-404	3	28
β-strand	405-407	3	27
α-helix	409-412	4
β-strand	417-419	3	29
β-strand	426-428	3	29
β-strand	429-432	4	25
β-strand	442	1	30
β-strand	445	1	30
β-strand	450-452	3	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3	C, D, E	protein	1663	Homo sapiens	P01024 (AlphaFold model)
Complement factor B Bb	B	protein	505	Homo sapiens	P00751 (AlphaFold model)
Properdin	P	protein	453	Homo sapiens	P27918 (AlphaFold model)

Sequence of entity 1 (C, D, E), FASTA

>9U62_1 Complement C3 (chains C, D, E)
MGPTSGPSLLLLLLTHLPLALGSPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVH
DFPGKKLVLSSEKTVLTPATNHMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKV
VLVSLQSGYLFIQTDKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSL
SSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTE
KFYYIYNEKGLEVTITARFLYGKKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEV
VLSRKVLLDGVQNPRAEDLVGKSLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKT
PKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPL
SITVRTKKQELSEAEQATRTMQALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMD
RAHEAKIRYYTYLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGA
SGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDK
GVFVLNKKNKLTQSKIWDVVEKADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAEL
QCPQPAARRRRSVQLTEKRMDKVGKYPKELRKCCEDGMRENPMRFSCQRRTRFISLGEAC
KKVFLDCCNYITELRRQHARASHLGLARSNLDEDIIAEENIVSRSEFPESWLWNVEDLKE
PPKNGISTKLMNIFLKDSITTWEILAVSMSDKKGICVADPFEVTVMQDFFIDLRLPYSVV
RNEQVEIRAVLYNYRQNQELKVRVELLHNPAFCSLATTKRRHQQTVTIPPKSSLSVPYVI
VPLKTGLQEVEVKAAVYHHFISDGVRKSLKVVPEGIRMNKTVAVRTLDPERLGREGVQKE
DIPPADLSDQVPDTESETRILLQGTPVAQMTEDAVDAERLKHLIVTPSGCGEQNMIGMTP
TVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTA
YVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKD
MALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMG
RLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQR
YYGGGYGSTQATFMVFQALAQYQKDAPDHQELNLDVSLQLPSRSSKITHRIHWESASLLR
SEETKENEGFTVTAEGKGQGTLSVVTMYHAKAKDQLTCNKFDLKVTIKPAPETEKRPQDA
KNTMILEICTRYRGDQDATMSILDISMMTGFAPDTDDLKQLANGVDRYISKYELDKAFSD
RNTLIIYLDKVSHSEDDCLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDG
KLNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDE
YIMAIEQTIKSGSDEVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSY
IIGKDTWVEHWPEEDECQDEENQKQCQDLGAFTESMVVFGCPN

Sequence of entity 2 (B), FASTA

>9U62_2 Complement factor B Bb (chains B)
KIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPK
IWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNR
TRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNI
NALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKI
SVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNY
NINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQK
EELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPR
FLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHAR
DFHINLFQVLPWLKEKLQDEDLGFL

Sequence of entity 3 (P), FASTA

>9U62_3 Properdin (chains P)
MITEGAQAPRLLLPPLLLLLTLPATGSDPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNT
AFAYQKRSGGLCQPCRSPRWSLWSTWAPCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTL
EWQLQACEDQQCCPEMGGWSGWGPWEPCSVTCSKGTRTRRRACNHPAPKCGGHCPGQAQE
SEACDTQQVCPTHGAWATWGPWTPCSASCHGGPHEPKETRSRKCSAPEPSQKPPGKPCPG
LAYEQRRCTGLPPCPVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDA
TRTHICNTAVPCPVDGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRC
AGQQQDIRHCYSIQHCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSM
VEGQGEKNVTFWGRPLPRCEELQGQKLVVEEKR

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Complement C3 Recognition by C3 Convertases. Yang, X.K., Xiao, J.Y. Sci Adv (2026).

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

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