9U5Z: C3 convertases zymogen C4b2 in activation state

C3 convertases zymogen C4b2 in activation state. Determined by electron microscopy at 3.1 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 16,448
Mol. weight: 276.4 kDa
Ligands: NI
Released: 14 Jan 2026

Explore 9U5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U5Z contains 46 α-helices and 154 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: 20 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	1
β-strand	34-37	4	2
β-strand	46	1	3
β-strand	47-50	4	2
β-strand	55-56	2	4
β-strand	63	1	3
β-strand	83	1	1
β-strand	85-86	2	4
β-strand	89	1	5
α-helix	90-92	3
β-strand	98-100	3	6
β-strand	107	1	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
β-strand	161-163	3	10
β-strand	172-176	5	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	213-230	18
β-strand	253-259	7	13
α-helix	271-284	14
β-strand	292-297	6	13
β-strand	303-304	2	13
α-helix	311-313	3
α-helix	316-323	8
α-helix	329-332	4
α-helix	339-350	12
α-helix	352	1
β-strand	368-374	7	13
α-helix	386-395	10
β-strand	408-414	7	13
α-helix	420-426	7
β-strand	436-438	3	13
α-helix	447-449	3
β-strand	481-484	4	14
β-strand	492-496	5	14
β-strand	501-504	4	14
β-strand	534-539	6	14
β-strand	563-567	5	14
α-helix	570-573	4
β-strand	581	1	15
α-helix	582	1
α-helix	586-592	7
α-helix	602-605	4
β-strand	611-612	2	15
β-strand	616-618	3	16
β-strand	624-626	3	16
β-strand	629-630	2	15
α-helix	635-639	5
α-helix	642-644	3
β-strand	663-666	4	15
α-helix	676-678	3
α-helix	681	1
β-strand	682-686	5	15
β-strand	691-700	10	15
β-strand	706	1	17
β-strand	709	1	17
β-strand	727-731	5	15
α-helix	736-742	7

Chain E: 26 helices, 107 β-strands

Element	Residues	Length	Sheet
β-strand	23-28	6	18
β-strand	30-31	2	19
β-strand	37-43	7	18
β-strand	50-52	3	20
β-strand	55-58	4	19
β-strand	62-66	5	19
β-strand	71-73	3	20
α-helix	75-77	3
β-strand	80-85	6	18
β-strand	108-115	8	19
β-strand	126-128	3	19
α-helix	129-130	2
β-strand	132-134	3	19
β-strand	140-145	6	21
β-strand	149-150	2	22
β-strand	155-163	9	21
β-strand	169	1	21
β-strand	173-179	7	22
β-strand	185-192	8	22
β-strand	197	1	21
β-strand	200-203	4	21
α-helix	204-205	2
β-strand	211-219	9	22
β-strand	227-233	7	22
β-strand	241-246	6	23
β-strand	252-254	3	24
β-strand	262-270	9	23
β-strand	275	1	23
β-strand	278-288	11	24
β-strand	292-295	4	24
β-strand	301-305	5	24
β-strand	306	1	23
β-strand	309-314	6	23
α-helix	316-322	7
α-helix	323-325	3
β-strand	337-346	10	24
β-strand	352-363	12	24
β-strand	368-370	3	25
β-strand	377	1	26
β-strand	383-391	9	25
β-strand	397	1	25
β-strand	402-405	4	27
β-strand	423-424	2	27
β-strand	430-436	7	25
β-strand	444-450	7	27
β-strand	457-462	6	27
β-strand	463	1	26
β-strand	474-477	4	28
β-strand	487-495	9	28
β-strand	504-511	8	29
β-strand	514-522	9	29
β-strand	527-533	7	28
α-helix	535-537	3
β-strand	540-549	10	29
β-strand	552-561	10	29
β-strand	571	1	30
β-strand	574	1	31
β-strand	581	1	32
β-strand	588-589	2	31
β-strand	592	1	30
β-strand	598-605	8	33
α-helix	607-611	5
α-helix	621-629	9
β-strand	638	1	29
α-helix	643-650	8
β-strand	652-656	5	18
β-strand	660	1	18
α-helix	769-771	3
β-strand	775	1	34
β-strand	781-782	2	33
β-strand	786-788	3	33
β-strand	795-796	2	31
β-strand	805-813	9	33
β-strand	819-821	3	33
α-helix	822-824	3
β-strand	825-828	4	33
β-strand	829	1	32
β-strand	834-838	5	35
β-strand	842-843	2	34
β-strand	850-851	2	36
β-strand	852-857	6	35
β-strand	863-869	7	34
β-strand	875	1	37
β-strand	885-889	5	34
β-strand	893-896	4	35
β-strand	899-900	2	36
β-strand	903	1	37
β-strand	908-915	8	34
β-strand	925-933	9	34
β-strand	938-940	3	38
β-strand	944-947	4	39
β-strand	956-959	4	40
α-helix	960-962	3
β-strand	968	1	38
β-strand	976-980	5	39
α-helix	994-996	3
α-helix	1019-1030	12
α-helix	1041-1055	15
α-helix	1072-1082	11
α-helix	1103-1106	4
α-helix	1140-1153	14
α-helix	1171-1181	11
α-helix	1190-1200	11
α-helix	1279-1286	8
α-helix	1300-1307	8
α-helix	1311-1316	6
β-strand	1324-1327	4	40
β-strand	1342-1345	4	40
β-strand	1355-1357	3	39
β-strand	1365-1368	4	40
β-strand	1377-1382	6	39
β-strand	1384-1386	3	38
β-strand	1397-1405	9	41
β-strand	1465-1474	10	41
β-strand	1484-1488	5	42
β-strand	1494-1496	3	41
α-helix	1498-1505	8
β-strand	1510-1511	2	42
β-strand	1522-1526	5	42
β-strand	1534-1542	9	41
β-strand	1552-1558	7	42
β-strand	1568-1570	3	42
β-strand	1580	1	43
β-strand	1590	1	43
α-helix	1612-1617	6
β-strand	1627-1635	9	44
β-strand	1641-1649	9	44
β-strand	1666-1669	4	44
β-strand	1682-1686	5	44
β-strand	1693	1	44
β-strand	1700-1702	3	44
β-strand	1708-1711	4	44
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

>9U5Z_1 Complement C2 (chains B)
MGPLMVLFCLLFLYPGLADSAPSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPA
SRLCKSSGQWQTPGATRSLSKAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDG
FILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSN
LVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVAPALGTSFSHMLGATNPTQKTKES
LGRKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFAS
EPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGME
TMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDW
RELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPW
HVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVI
SPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTC
RDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVT
DQFLCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRS
KVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL

Sequence of entity 2 (E), FASTA

>9U5Z_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
9U60 2.9 Å, C3 convertases zymogen C4b2 in loading 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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