9U60: C3 convertases zymogen C4b2 in loading state

C3 convertases zymogen C4b2 in loading state. Determined by electron microscopy at 2.9 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 14,725
Mol. weight: 276.4 kDa
Ligands: NI
Released: 14 Jan 2026

Explore 9U60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U60 contains 54 α-helices and 139 β-strands across 2 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: 13 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	1
β-strand	34-37	4	2
β-strand	47-50	4	2
β-strand	55-57	3	3
β-strand	62	1	2
β-strand	63-64	2	4
β-strand	70-71	2	4
β-strand	82-83	2	1
β-strand	84-86	3	3
β-strand	89-90	2	5
α-helix	91-92	2
β-strand	98-100	3	6
β-strand	106-107	2	5
β-strand	112-114	3	7
β-strand	115-117	3	6
β-strand	122-124	3	8
β-strand	128-130	3	7
β-strand	131	1	9
β-strand	137	1	9
β-strand	143-145	3	8
α-helix	152-153	2
β-strand	160-163	4	10
β-strand	172-177	6	10
β-strand	182-184	3	11
β-strand	188-190	3	10
β-strand	191	1	12
β-strand	197	1	12
β-strand	203-205	3	11
α-helix	213-225	13
β-strand	253-260	8	13
α-helix	267-286	20
β-strand	291-298	8	13
β-strand	303-306	4	13
α-helix	311-314	4
α-helix	316-324	9
α-helix	328-331	4
α-helix	339-357	19
α-helix	362-366	5
β-strand	368-375	8	13
α-helix	386-395	10
α-helix	403-405	3
β-strand	406-413	8	13
α-helix	420-426	7
β-strand	436-439	4	13
α-helix	442-448	7

Chain E: 41 helices, 107 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	14
β-strand	30-32	3	15
β-strand	37-44	8	14
β-strand	51-59	9	15
β-strand	67	1	15
β-strand	72-77	6	15
β-strand	83-87	5	14
α-helix	91-96	6
β-strand	107-113	7	15
α-helix	116-119	4
β-strand	127-135	9	15
β-strand	140-145	6	16
β-strand	149-150	2	17
β-strand	155-163	9	16
β-strand	169	1	16
β-strand	174-179	6	17
β-strand	184-191	8	17
β-strand	197-203	7	16
β-strand	211-219	9	17
β-strand	227-233	7	17
β-strand	241-247	7	18
β-strand	251-253	3	19
β-strand	262-270	9	18
β-strand	275	1	18
β-strand	278-287	10	19
β-strand	293-304	12	19
β-strand	306	1	18
β-strand	309-314	6	18
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	19
β-strand	352-357	6	19
β-strand	361-363	3	19
β-strand	367-370	4	20
β-strand	377	1	21
β-strand	384-392	9	20
β-strand	397	1	20
β-strand	402-410	9	21
β-strand	417-424	8	21
β-strand	430-435	6	20
β-strand	443-449	7	21
β-strand	457-463	7	21
α-helix	464-466	3
β-strand	472-476	5	22
α-helix	482-483	2
β-strand	488-496	9	22
β-strand	504-511	8	23
β-strand	514-522	9	23
β-strand	528-532	5	22
α-helix	535-537	3
β-strand	540-549	10	23
β-strand	552-561	10	23
α-helix	562-564	3
β-strand	571-575	5	24
β-strand	581	1	25
β-strand	586-605	20	24
α-helix	606-610	5
α-helix	621-628	8
α-helix	629-631	3
α-helix	643-650	8
β-strand	652-655	4	14
β-strand	660	1	14
α-helix	661-664	4
α-helix	763-765	3
β-strand	766	1	26
α-helix	767-768	2
α-helix	769-771	3
β-strand	775	1	27
β-strand	781-798	18	24
β-strand	805-814	10	24
β-strand	818-821	4	24
α-helix	822-824	3
β-strand	825-828	4	24
β-strand	829	1	25
β-strand	834-837	4	28
α-helix	838-840	3
β-strand	844	1	29
β-strand	849-851	3	30
β-strand	853-856	4	28
β-strand	863-869	7	27
β-strand	875-876	2	31
β-strand	885-889	5	27
β-strand	894-896	3	28
β-strand	899-901	3	30
β-strand	902-903	2	31
β-strand	908-916	9	27
β-strand	918	1	26
β-strand	924-932	9	27
β-strand	934	1	29
α-helix	935	1
β-strand	938-948	11	17
β-strand	958-960	3	32
α-helix	961-963	3
β-strand	973-982	10	17
α-helix	996-1000	5
α-helix	1005-1007	3
α-helix	1014-1028	15
α-helix	1039-1055	17
α-helix	1072-1082	11
α-helix	1099-1109	11
α-helix	1138-1151	14
α-helix	1162-1182	21
α-helix	1190-1199	10
α-helix	1210-1217	8
β-strand	1224	1	33
β-strand	1227	1	33
α-helix	1260-1271	12
α-helix	1279-1288	10
β-strand	1327-1329	3	34
β-strand	1332-1334	3	32
β-strand	1339-1340	2	32
β-strand	1344-1345	2	34
β-strand	1353-1357	5	17
β-strand	1366-1368	3	32
β-strand	1370-1372	3	34
β-strand	1376-1386	11	17
β-strand	1397-1405	9	35
β-strand	1409	1	36
α-helix	1411-1413	3
β-strand	1465-1474	10	35
β-strand	1484-1489	6	37
β-strand	1494-1496	3	35
α-helix	1502-1506	5
β-strand	1512-1514	3	37
β-strand	1517	1	37
β-strand	1521-1526	6	37
β-strand	1534-1542	9	35
β-strand	1546	1	36
β-strand	1552-1558	7	37
β-strand	1567-1570	4	37
β-strand	1581-1584	4	38
β-strand	1587-1590	4	38
α-helix	1594-1596	3
β-strand	1598-1599	2	39
α-helix	1612-1618	7
α-helix	1622-1623	2
β-strand	1625-1635	11	39
β-strand	1640-1652	13	39
β-strand	1664-1670	7	39
β-strand	1682-1687	6	39
β-strand	1693	1	40
α-helix	1698	1
β-strand	1699	1	40
α-helix	1700	1
β-strand	1701-1702	2	39
β-strand	1708-1711	4	39
α-helix	1712-1713	2
α-helix	1724-1739	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C2	B	protein	752	Homo sapiens	P06681 (AlphaFold model)
Complement C4-B	E	protein	1744	Homo sapiens	P0C0L5 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9U60_1 Complement C2 (chains B)
MGPLMVLFCLLFLYPGLADSAPSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPA
SRLCKSSGQWQTPGATRSLSKAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDG
FILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSN
LVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVAPALGTSFSHMLGATNPTQKTKES
LGRKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFAS
EPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGME
TMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDW
RELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPW
HVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVI
SPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTC
RDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVT
DQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRS
KVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL

Sequence of entity 2 (E), FASTA

>9U60_2 Complement C4-B (chains E)
MRLLWGLIWASSFFTLSLQKPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRN
PSRNNVPCSPKVDFTLSSERDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDS
LSRTTNIQGINLLFSSRRGHLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVEN
SHGLRVRKKEVYMPSSIFQDDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPN
FEVKITPGKPYILTVPGHLDEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLE
SQTKLVNGQSHISLSKAEFQDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSW
YFVSSPFSLDLSKTKRHLVPGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQD
IQQNTDGSGQVSIPIIIPQTISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDS
RPPRVGDTLNLNLRAVGSGATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPS
FYFVAFYYHGDHPVANSLRVDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVA
LGALDTALYAAGSKSHKPLNMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQW
TLSRKRLSCPKEKTTRKKRNVNFQKAINEKLGQYASPTAKRCCQDGVTRLPMMRSCEQRA
ARVQQPDCREPFLSCCQFAESLRKKSRDKGQAGLQRALEILQEEDLIDEDDIPVRSFFPE
NWLWRVETVDRFQILTLWLPDSLTTWEIHGLSLSKTKGLCVATPVQLRVFREFHLHLRLP
MSVRRFEQLELRPVLYNYLDKNLTVSVHVSPVEGLCLAGGGGLAQQVLVPAGSARPVAFS
VVPTAATAVSLKVVARGSFEFPVGDAVSKVLQIEKEGAIHREELVYELNPLDHRGRTLEI
PGNSDPNMIPDGDFNSYVRVTASDPLDTLGSEGALSPGGVASLLRLPRGCGEQTMIYLAP
TLAASRYLDKTEQWSTLPPETKDHAVDLIQKGYMRIQQFRKADGSYAAWLSRGSSTWLTA
FVLKVLSLAQEQVGGSPEKLQETSNWLLSQQQADGSFQDLSPVIHRSMQGGLVGNDETVA
LTAFVTIALHHGLAVFQDEGAEPLKQRVEASISKASSFLGEKASAGLLGAHAAAITAYAL
TLTKAPADLRGVAHNNLMAMAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPAL
WIETTAYALLHLLLHEGKAEMADQAAAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASH
TTEERGLNVTLSSTGRNGFKSHALQLNNRQIRGLEEELQFSLGSKINVKVGGNSKGTLKV
LRTYNVLDMKNTTCQDLQIEVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTP
LQLFEGRRNRRRREAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRAD
LEKLTSLSDRYVSHFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYY
NPERRCSVFYGAPSKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYY
PRVEYGFQVKVLREDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPG
KEYLIMGLDGATYDLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQ
GCQV

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1

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 P06681 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ERB 1.8 Å, The Crystal Structure of C2b, a Fragment of Complement Component C2 produced during…
8ACF 1.8 Å, Structure of the argX-117 in complex with a complement C2 fragment at low pH
8ACI 1.85 Å, Structure of ARG-117 Fab in complex with a fragment of complement C2, neutral pH
2I6Q 2.1 Å, Complement component C2a
9ZCJ 2.6 Å, Therapeutic antibody with captured antigen
2I6S 2.7 Å, Complement component C2a
9U5Z 3.1 Å, C3 convertases zymogen C4b2 in activation state
9U61 3.1 Å, CP/MBL pathways C3 convertase C4b2a and C3 complex
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…
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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