9QJ5: Complement C4-A

Structure of the Complement classical and lectin pathway proconvertase, C4b2. Determined by electron microscopy at 3.5 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,950
Mol. weight: 663.07 kDa
Ligands: MG, NAG
Released: 24 Dec 2025

Explore 9QJ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QJ5 contains 50 α-helices and 133 β-strands across 4 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: 21 helices, 51 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	51-59	9	2
α-helix	60	1
β-strand	72-77	6	2
β-strand	82-87	6	1
α-helix	91-97	7
β-strand	107-113	7	2
α-helix	116	1
α-helix	117-121	5
β-strand	127-135	9	2
β-strand	140-145	6	3
β-strand	149-150	2	4
β-strand	155-163	9	3
β-strand	169	1	3
β-strand	174-179	6	4
β-strand	185-191	7	4
β-strand	197-203	7	3
α-helix	208-209	2
β-strand	211-219	9	4
β-strand	226-233	8	4
β-strand	241-247	7	5
β-strand	251-253	3	6
α-helix	260-261	2
β-strand	262-270	9	5
α-helix	274	1
β-strand	275	1	5
α-helix	276	1
β-strand	278-287	10	7
β-strand	293-295	3	7
β-strand	301-304	4	7
β-strand	306	1	5
β-strand	309-314	6	5
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	7
β-strand	352-357	6	7
β-strand	361-363	3	6
β-strand	367-370	4	8
α-helix	378-379	2
β-strand	384-392	9	8
β-strand	397	1	8
α-helix	398	1
β-strand	402-409	8	9
β-strand	417-424	8	9
β-strand	427	1	8
β-strand	430-435	6	8
β-strand	444-450	7	9
α-helix	455	1
β-strand	456-462	7	9
α-helix	465-466	2
β-strand	472-476	5	10
α-helix	482-484	3
β-strand	488-491	4	11
β-strand	492-496	5	10
β-strand	504-511	8	12
β-strand	514-522	9	12
β-strand	529-532	4	11
α-helix	535-537	3
β-strand	540-549	10	12
β-strand	552-561	10	12
β-strand	571-575	5	13
β-strand	581	1	14
β-strand	586-605	20	13
α-helix	607-611	5
α-helix	615-619	5
α-helix	621-629	9
α-helix	643-650	8
β-strand	652-655	4	1
β-strand	660	1	1
α-helix	661-664	4

Chain B: 7 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	766	1	20
α-helix	773	1
β-strand	774-775	2	21
β-strand	781-782	2	13
β-strand	786-798	13	13
β-strand	805-814	10	13
β-strand	819-821	3	13
α-helix	822-824	3
β-strand	825-828	4	13
β-strand	829	1	14
β-strand	833-837	5	22
β-strand	844	1	23
β-strand	849-851	3	24
β-strand	853-857	5	22
β-strand	863-869	7	21
β-strand	875-876	2	25
α-helix	878-881	4
β-strand	885-889	5	21
β-strand	893-896	4	22
β-strand	899-901	3	24
β-strand	902-903	2	25
β-strand	909-910	2	26
β-strand	913-917	5	21
β-strand	918	1	20
β-strand	924-927	4	21
β-strand	930-931	2	26
β-strand	934	1	23
α-helix	935	1
β-strand	938-948	11	4
α-helix	953-955	3
β-strand	957-960	4	27
α-helix	961-963	3
β-strand	968	1	4
α-helix	969	1
β-strand	975-980	6	4
β-strand	1330-1333	4	27
β-strand	1340-1343	4	27
β-strand	1356-1360	5	4
β-strand	1366-1369	4	27
β-strand	1376-1386	11	4
β-strand	1397-1404	8	15
β-strand	1409	1	17

Chain C: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1474	10	15
β-strand	1484-1489	6	16
β-strand	1494-1496	3	15
α-helix	1498-1505	8
β-strand	1514-1518	5	16
β-strand	1521-1526	6	16
β-strand	1534-1536	3	15
β-strand	1539-1542	4	15
β-strand	1546	1	17
β-strand	1552-1558	7	16
β-strand	1566-1570	5	16
β-strand	1581-1584	4	18
β-strand	1587-1590	4	18
β-strand	1599	1	19
α-helix	1606-1608	3
α-helix	1612-1618	7
α-helix	1622-1623	2
β-strand	1625-1637	13	19
β-strand	1640-1653	14	19
β-strand	1664-1670	7	19
β-strand	1682-1687	6	19
β-strand	1701-1702	2	19
β-strand	1708-1711	4	19
α-helix	1712-1713	2
α-helix	1723-1739	17

Chain D: 16 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	28
β-strand	34-37	4	29
β-strand	46-50	5	29
β-strand	55-56	2	30
β-strand	61-63	3	29
α-helix	70	1
β-strand	71	1	29
β-strand	83	1	28
β-strand	85-86	2	30
α-helix	87	1
β-strand	88	1	31
α-helix	89-91	3
β-strand	98-101	4	32
β-strand	108	1	31
β-strand	112-117	6	32
β-strand	122-124	3	33
β-strand	128-130	3	32
α-helix	141-142	2
β-strand	143-145	3	33
β-strand	160-163	4	34
β-strand	172-177	6	34
β-strand	182-184	3	35
β-strand	188-190	3	34
β-strand	191	1	36
β-strand	197	1	36
α-helix	200-202	3
β-strand	203-205	3	35
α-helix	213-228	16
β-strand	252-260	9	37
α-helix	267-286	20
β-strand	291-298	8	37
β-strand	303-304	2	37
α-helix	311-314	4
α-helix	316-324	9
α-helix	329-331	3
α-helix	339-357	19
α-helix	362-365	4
β-strand	367-375	9	37
α-helix	385-396	12
α-helix	402-405	4
β-strand	406-413	8	37
α-helix	420-426	7
β-strand	436-439	4	37
α-helix	442-450	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C4-A	A, B, C	protein	1744	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C2	D	protein	752	Homo sapiens	P06681 (AlphaFold model)

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

>9QJ5_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
TLTKAPVDLLGVAHNNLMAMAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPAL
WIETTAYALLHLLLHEGKAEMADQASAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASH
TTEERGLNVTLSSTGRNGFKSHALQLNNRQIRGLEEELQFSLGSKINVKVGGNSKGTLKV
LRTYNVLDMKNTTCQDLQIEVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTP
LQLFEGRRNRRRREAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRAD
LEKLTSLSDRYVSHFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYY
NPERRCSVFYGAPSKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYY
PRVEYGFQVKVLREDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPG
KEYLIMGLDGATYDLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQ
GCQV

Sequence of entity 2 (D), FASTA

>9QJ5_2 Complement C2 (chains D)
MGPLMVLFCLLFLYPGLADSAPSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPA
SRLCKSSGQWQTPGATRSLSKAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDG
FILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSN
LVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVAPALGTSFSHMLGATNPTQKTKES
LGRKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFAS
EPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGME
TMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDW
RELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPW
HVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVI
SPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTC
RDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVT
DQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRS
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	3

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
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
9QPY 4.3 Å, Structure of the Complement classical and lectin pathway C3 convertase

Browse structure collections

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