9QPY: Complement C4-A

Structure of the Complement classical and lectin pathway C3 convertase. Determined by electron microscopy at 4.3 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 4.3 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 16,917
Mol. weight: 677.22 kDa
Ligands: MG, NAG
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9QPY contains 63 α-helices and 153 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 A: 17 helices, 62 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	30-32	3	2
β-strand	37-44	8	1
β-strand	51	1	3
β-strand	55-60	6	2
α-helix	61-63	3
β-strand	66-67	2	2
β-strand	72-73	2	2
β-strand	77	1	3
β-strand	82-87	6	1
α-helix	91-97	7
α-helix	99-101	3
β-strand	107-113	7	2
α-helix	116-119	4
β-strand	127-135	9	2
β-strand	140-145	6	4
β-strand	149-150	2	5
β-strand	155-163	9	4
β-strand	169	1	4
β-strand	173-179	7	6
β-strand	185-192	8	6
β-strand	197-203	7	4
α-helix	208-209	2
β-strand	211-212	2	5
β-strand	214-219	6	6
β-strand	227-229	3	6
β-strand	232-233	2	5
β-strand	241-247	7	7
β-strand	252-253	2	8
β-strand	262-270	9	7
β-strand	275	1	7
β-strand	279-287	9	9
β-strand	293-295	3	9
β-strand	301-304	4	9
β-strand	306	1	7
β-strand	309-314	6	7
α-helix	316-326	11
α-helix	330-332	3
β-strand	337-342	6	9
β-strand	345	1	9
β-strand	352	1	9
β-strand	355-356	2	9
β-strand	361	1	9
β-strand	362-363	2	8
β-strand	367-370	4	10
β-strand	384	1	11
β-strand	387-392	6	10
α-helix	396	1
β-strand	397	1	10
α-helix	398	1
β-strand	402-410	9	12
α-helix	415-416	2
β-strand	417-424	8	12
β-strand	430-432	3	10
β-strand	435	1	11
β-strand	443-450	8	12
β-strand	456-463	8	12
α-helix	464-466	3
β-strand	473-476	4	13
α-helix	483-484	2
β-strand	488-495	8	13
β-strand	504-511	8	14
β-strand	514-522	9	14
β-strand	527-532	6	13
β-strand	540-541	2	15
β-strand	542-549	8	14
β-strand	552-557	6	14
β-strand	560-561	2	15
β-strand	572-574	3	16
α-helix	581-582	2
β-strand	586-589	4	17
β-strand	590-592	3	16
β-strand	597-604	8	18
α-helix	607-610	4
α-helix	621-629	9
α-helix	643-649	7
β-strand	652-655	4	1
β-strand	660	1	1
α-helix	661-664	4

Chain B: 16 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	774-775	2	19
β-strand	784-789	6	18
β-strand	795-798	4	17
β-strand	805-809	5	18
β-strand	811-814	4	18
β-strand	819-821	3	18
α-helix	822-824	3
β-strand	825-828	4	18
β-strand	833-836	4	20
β-strand	850-851	2	21
β-strand	854-857	4	20
β-strand	863-869	7	19
α-helix	870-871	2
β-strand	875-876	2	22
β-strand	885-889	5	19
β-strand	893-896	4	20
β-strand	899-900	2	21
β-strand	902-903	2	22
β-strand	908-916	9	19
β-strand	925-932	8	19
β-strand	938-948	11	6
β-strand	959-960	2	23
α-helix	961-963	3
β-strand	975-981	7	6
α-helix	997-1001	5
α-helix	1015-1031	17
α-helix	1041-1057	17
α-helix	1073-1074	2
α-helix	1076-1089	14
α-helix	1097-1108	12
β-strand	1111	1	24
β-strand	1117	1	24
α-helix	1138-1155	18
α-helix	1162-1185	24
α-helix	1190-1202	13
α-helix	1207-1220	14
α-helix	1259-1274	16
α-helix	1282-1293	12
α-helix	1303-1319	17
β-strand	1328	1	25
β-strand	1329-1335	7	23
β-strand	1338-1344	7	23
β-strand	1356	1	6
β-strand	1359-1360	2	6
β-strand	1366-1368	3	23
β-strand	1371	1	25
β-strand	1376-1386	11	6
β-strand	1397-1405	9	26
β-strand	1409	1	27

Chain C: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	1466-1474	9	26
β-strand	1484-1486	3	28
β-strand	1489	1	28
β-strand	1494-1496	3	26
α-helix	1498-1506	9
β-strand	1512-1518	7	28
β-strand	1521-1526	6	28
β-strand	1536-1542	7	26
β-strand	1546	1	27
β-strand	1552-1558	7	28
β-strand	1561-1570	10	28
β-strand	1581	1	29
β-strand	1590	1	29
α-helix	1613-1618	6
β-strand	1625-1637	13	30
β-strand	1640-1652	13	30
β-strand	1664-1670	7	30
β-strand	1682-1687	6	30
α-helix	1698-1700	3
β-strand	1701-1702	2	30
β-strand	1708-1711	4	30
α-helix	1721-1723	3
α-helix	1727-1739	13

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	13	1	32
β-strand	19-24	6	31
β-strand	31-35	5	33
β-strand	42-47	6	33
β-strand	54-56	3	33
α-helix	58-60	3
β-strand	65-68	4	31
β-strand	74-78	5	31
β-strand	88-93	6	33
β-strand	94	1	34
β-strand	108	1	34
β-strand	114-116	3	33
β-strand	119	1	32

Chain E: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	245-246	2	35
β-strand	253-260	8	36
α-helix	267-285	19
β-strand	291-298	8	36
β-strand	302-304	3	36
α-helix	311-314	4
α-helix	316-325	10
α-helix	328-331	4
α-helix	339-357	19
α-helix	362-365	4
β-strand	368-374	7	36
α-helix	385-396	12
α-helix	400-405	6
β-strand	406-413	8	36
α-helix	420-426	7
β-strand	430	1	37
β-strand	433	1	37
β-strand	436-439	4	36
α-helix	442-450	9
β-strand	453-454	2	35
α-helix	474-477	4
β-strand	481-485	5	38
β-strand	492-496	5	38
β-strand	501-504	4	38
α-helix	506-508	3
α-helix	515-517	3
β-strand	519-524	6	38
β-strand	527-533	7	38
β-strand	535-540	6	38
α-helix	550-552	3
β-strand	563-567	5	38
β-strand	581	1	39
α-helix	582	1
β-strand	585	1	40
α-helix	586-591	6
α-helix	600-607	8
β-strand	612-618	7	39
β-strand	624-630	7	39
α-helix	632-639	8
α-helix	640-644	5
β-strand	663	1	39
β-strand	666	1	39
α-helix	676-678	3
β-strand	682-687	6	39
β-strand	690-700	11	39
α-helix	724-725	2
β-strand	727-731	5	39
α-helix	733-735	3
α-helix	736-743	8
β-strand	749	1	40
α-helix	750-751	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C4-A	A, B, C	protein	1744	Homo sapiens	P0C0L4 (AlphaFold model)
Anti-C4b nanobody B12	D	protein	120	Lama glama
Complement C2	E	protein	752	Homo sapiens	P06681 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9QPY_1 Complement C4-A (chains A, B, C)
MRLLWGLIWASSFFTLSLQKPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRN
PSRNNVPCSPKVDFTLSSERDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDS
LSRTTNIQGINLLFSSRRGHLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVEN
SHGLRVRKKEVYMPSSIFQDDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPN
FEVKITPGKPYILTVPGHLDEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLE
SQTKLVNGQSHISLSKAEFQDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSW
YFVSSPFSLDLSKTKRHLVPGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQD
IQQNTDGSGQVSIPIIIPQTISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDS
RPPRVGDTLNLNLRAVGSGATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPS
FYFVAFYYHGDHPVANSLRVDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVA
LGALDTALYAAGSKSHKPLNMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQW
TLSRKRLSCPKEKTTRKKRNVNFQKAINEKLGQYASPTAKRCCQDGVTRLPMMRSCEQRA
ARVQQPDCREPFLSCCQFAESLRKKSRDKGQAGLQRALEILQEEDLIDEDDIPVRSFFPE
NWLWRVETVDRFQILTLWLPDSLTTWEIHGLSLSKTKGLCVATPVQLRVFREFHLHLRLP
MSVRRFEQLELRPVLYNYLDKNLTVSVHVSPVEGLCLAGGGGLAQQVLVPAGSARPVAFS
VVPTAAAAVSLKVVARGSFEFPVGDAVSKVLQIEKEGAIHREELVYELNPLDHRGRTLEI
PGNSDPNMIPDGDFNSYVRVTASDPLDTLGSEGALSPGGVASLLRLPRGCGEQTMIYLAP
TLAASRYLDKTEQWSTLPPETKDHAVDLIQKGYMRIQQFRKADGSYAAWLSRDSSTWLTA
FVLKVLSLAQEQVGGSPEKLQETSNWLLSQQQADGSFQDPCPVLDRSMQGGLVGNDETVA
LTAFVTIALHHGLAVFQDEGAEPLKQRVEASISKANSFLGEKASAGLLGAHAAAITAYAL
SLTKAPVDLLGVAHNNLMAMAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPAL
WIETTAYALLHLLLHEGKAEMADQASAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASH
TTEERGLNVTLSSTGRNGFKSHALQLNNRQIRGLEEELQFSLGSKINVKVGGNSKGTLKV
LRTYNVLDMKNTTCQDLQIEVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTP
LQLFEGRRNRRRREAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRAD
LEKLTSLSDRYVSHFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYY
NPERRCSVFYGAPSKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYY
PRVEYGFQVKVLREDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPG
KEYLIMGLDGATYDLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQ
GCQV

Sequence of entity 2 (D), FASTA

>9QPY_2 Anti-C4b nanobody B12 (chains D)
EVQLVESGGGLVQAGGSLRLSCVASERTYMAWFRQAPGKEREFVAAITSSGMMTEYAPSV
KGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADLRQRFGERVTEYDYWGQGTQVTVSS

Sequence of entity 3 (E), FASTA

>9QPY_3 Complement C2 (chains E)
MGPLMVLFCLLFLYPGLADSAPSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPA
SRLCKSSGQWQTPGATRSLSKAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDG
FILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSN
LVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVAPALGTSFSHMLGATNPTQKTKES
LGRKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFAS
EPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGME
TMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDW
RELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPW
HVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVI
SPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTC
RDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVT
DQFLCSGTQEDESPCKGEAGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRS
KVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Structural insights into C3 convertase activity of the classical pathway of complement. De la O Becerra, K.I., Brondijk, T.H.C., Serna Martin, I. et al. Nat Commun (2025) 17:993-993. DOI 10.1038/s41467-025-67730-4 · PubMed

Other PDB entries of the same protein (UniProt P0C0L4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HZF 2.3 Å, C4ADG fragment of human complement factor C4A
6YSQ 3.3 Å, The hC4Nb8 complement inhibitory nanobody in complex with C4b
7B2M 3.39 Å, Cryo-EM structure of complement C4b in complex with nanobody E3
7B2P 3.43 Å, Cryo-EM structure of complement C4b in complex with nanobody B5
5JTW 3.5 Å, Crystal structure of complement C4b re-refined using iMDFF
9QJ5 3.5 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QK2 3.5 Å, Structure of the Complement classical and lectin pathway C3 convertase in complex with…
5JPN 3.6 Å, Structure of human complement C4 rebuilt using iMDFF
5JPM 3.75 Å, Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF
7B2Q 3.76 Å, Cryo-EM structure of complement C4b in complex with nanobody B12
9QJ4 3.9 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2

Browse structure collections

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