9U61: Serine protease complement C2b

CP/MBL pathways C3 convertase C4b2a and C3 complex. Determined by electron microscopy at 3.1 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 29,001
Mol. weight: 627.33 kDa
Ligands: NAG, NI
Released: 14 Jan 2026

Explore 9U61 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U61 contains 113 α-helices and 235 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 B: 17 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	245-246	2	1
β-strand	252-260	9	2
α-helix	267-284	18
β-strand	291-298	8	2
β-strand	302-304	3	2
α-helix	311-314	4
α-helix	316-325	10
β-strand	338	1	3
α-helix	340-357	18
β-strand	367-374	8	2
β-strand	381	1	3
α-helix	385-395	11
β-strand	406-412	7	2
α-helix	420-426	7
β-strand	436-438	3	2
α-helix	442-450	9
β-strand	453-454	2	1
α-helix	474-477	4
β-strand	481-485	5	4
β-strand	492-496	5	4
β-strand	501-504	4	4
α-helix	506-508	3
β-strand	519-522	4	4
β-strand	531-533	3	4
β-strand	535-540	6	4
β-strand	563-567	5	4
α-helix	570-573	4
β-strand	581	1	5
α-helix	582	1
β-strand	585	1	6
α-helix	586-592	7
α-helix	600-607	8
β-strand	612-618	7	5
β-strand	624-630	7	5
α-helix	634-639	6
α-helix	655-658	4
β-strand	663-666	4	5
β-strand	679	1	4
β-strand	682-686	5	5
β-strand	691-700	10	5
α-helix	715-718	4
β-strand	727-731	5	5
α-helix	736-742	7
β-strand	749	1	6

Chain C: 15 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	50
β-strand	33-35	3	51
β-strand	39-47	9	50
β-strand	53-59	7	51
β-strand	70-76	7	51
α-helix	78-80	3
β-strand	83-89	7	50
β-strand	105-112	8	51
β-strand	115-124	10	51
α-helix	125-127	3
β-strand	129-134	6	52
β-strand	138-139	2	53
β-strand	144-152	9	52
β-strand	158	1	52
β-strand	162-168	7	53
β-strand	174-181	8	53
β-strand	188-194	7	52
β-strand	202-210	9	53
β-strand	218-224	7	53
β-strand	233-238	6	54
β-strand	243-244	2	55
β-strand	251-258	8	54
β-strand	264	1	54
β-strand	267-276	10	56
β-strand	282-283	2	56
β-strand	289-293	5	56
β-strand	296-301	6	54
α-helix	306-310	5
α-helix	316-319	4
β-strand	323-332	10	56
β-strand	338-347	10	56
β-strand	348-349	2	55
β-strand	354-357	4	57
β-strand	363-364	2	58
β-strand	370-377	8	57
α-helix	382	1
β-strand	383	1	57
α-helix	384	1
β-strand	388-391	4	59
β-strand	394-400	7	59
β-strand	406-411	6	57
β-strand	420-426	7	59
α-helix	433-435	3
β-strand	438-443	6	59
β-strand	444-445	2	58
α-helix	446-447	2
β-strand	455-459	5	60
α-helix	464	1
β-strand	465	1	61
β-strand	470-478	9	60
α-helix	484-486	3
β-strand	489-496	8	62
β-strand	499-507	9	62
β-strand	514-520	7	60
α-helix	523-525	3
β-strand	528-538	11	62
β-strand	544-554	11	62
β-strand	555	1	61
β-strand	564-567	4	9
β-strand	580-587	8	9
β-strand	592-599	8	7
α-helix	600-605	6
α-helix	613-621	9
α-helix	635-641	7
β-strand	645-648	4	50
β-strand	653	1	50
α-helix	654-657	4

Chain D: 40 helices, 54 β-strands

Element	Residues	Length	Sheet
α-helix	676-682	7
α-helix	691-697	7
α-helix	700-701	2
α-helix	707-710	4
α-helix	711-713	3
α-helix	718-742	25
β-strand	747	1	5
α-helix	762-764	3
α-helix	768-770	3
β-strand	771-777	7	7
α-helix	781-782	2
β-strand	783	1	8
β-strand	786	1	8
β-strand	787-794	8	9
β-strand	801-810	10	7
β-strand	814-817	4	7
α-helix	818-820	3
β-strand	821-824	4	7
β-strand	829-834	6	10
β-strand	838-840	3	11
β-strand	844-853	10	10
β-strand	860-866	7	11
β-strand	872-873	2	12
β-strand	882-888	7	11
β-strand	892-900	9	10
β-strand	901-902	2	12
β-strand	906-916	11	11
β-strand	922-932	11	11
β-strand	936-947	12	13
β-strand	957-962	6	14
α-helix	963-965	3
β-strand	970	1	13
α-helix	971	1
β-strand	977-983	7	13
α-helix	988-994	7
α-helix	997-1000	4
α-helix	1001-1003	3
α-helix	1013-1017	5
α-helix	1019-1031	13
α-helix	1034-1037	4
α-helix	1041-1056	16
α-helix	1057-1059	3
β-strand	1060	1	15
β-strand	1066	1	15
β-strand	1067	1	16
β-strand	1074	1	16
α-helix	1076-1088	13
α-helix	1097-1109	13
β-strand	1112	1	17
β-strand	1118	1	17
α-helix	1127-1130	4
α-helix	1133-1135	3
α-helix	1137-1153	17
α-helix	1165-1178	14
α-helix	1186-1199	14
α-helix	1205-1212	8
β-strand	1215	1	18
β-strand	1219	1	18
α-helix	1226-1242	17
α-helix	1249-1258	10
α-helix	1270-1285	16
β-strand	1293-1299	7	14
β-strand	1307-1312	6	14
β-strand	1319-1324	6	13
β-strand	1330-1337	8	14
β-strand	1340-1350	11	13
α-helix	1351	1
β-strand	1361-1369	9	19
α-helix	1370-1371	2
β-strand	1382-1392	11	19
β-strand	1398	1	20
β-strand	1401-1406	6	21
β-strand	1411-1413	3	19
α-helix	1415-1423	9
β-strand	1431-1434	4	21
β-strand	1443-1448	6	21
β-strand	1451	1	20
β-strand	1457-1465	9	19
β-strand	1469-1470	2	10
β-strand	1475-1481	7	21
β-strand	1488-1493	6	21
α-helix	1511-1514	4
α-helix	1529-1535	7
β-strand	1543-1553	11	22
β-strand	1558-1570	13	22
β-strand	1581-1587	7	22
α-helix	1588-1590	3
α-helix	1591-1594	4
β-strand	1600-1606	7	22
β-strand	1611-1612	2	22
β-strand	1619-1621	3	22
β-strand	1627-1631	5	22
α-helix	1634-1636	3
α-helix	1640-1658	19

Chain E: 41 helices, 102 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	23
β-strand	30-32	3	24
β-strand	37-44	8	23
β-strand	52-56	5	25
β-strand	57-59	3	24
β-strand	67	1	24
β-strand	72-76	5	25
β-strand	82-87	6	23
α-helix	91-96	6
β-strand	107-111	5	24
α-helix	116-119	4
β-strand	129-135	7	24
β-strand	140-145	6	26
β-strand	149-150	2	27
β-strand	155-163	9	26
β-strand	169	1	26
β-strand	174-179	6	27
β-strand	184-191	8	27
β-strand	197-203	7	26
α-helix	208-209	2
β-strand	211-219	9	27
β-strand	226-233	8	27
β-strand	241-247	7	28
β-strand	252-253	2	29
β-strand	263-270	8	28
β-strand	275	1	28
β-strand	278-287	10	30
β-strand	293-304	12	30
β-strand	306	1	28
β-strand	309-313	5	28
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	30
β-strand	352-361	10	30
β-strand	362-363	2	29
β-strand	367-370	4	31
β-strand	384-392	9	31
β-strand	397	1	31
β-strand	402-410	9	32
β-strand	417-424	8	32
β-strand	430-435	6	31
β-strand	443-449	7	32
β-strand	457-463	7	32
α-helix	464-466	3
β-strand	475-476	2	33
α-helix	482-484	3
β-strand	488-493	6	33
β-strand	504-511	8	34
β-strand	514-522	9	34
β-strand	527-532	6	33
α-helix	535-537	3
β-strand	540-549	10	34
β-strand	552-561	10	34
α-helix	562-564	3
β-strand	572-574	3	35
β-strand	580-581	2	36
β-strand	586	1	37
β-strand	589-592	4	35
β-strand	596-605	10	36
α-helix	606-609	4
α-helix	621-628	8
α-helix	629-631	3
α-helix	643-650	8
β-strand	652-655	4	23
β-strand	660	1	23
β-strand	766	1	38
α-helix	767-768	2
α-helix	769-771	3
α-helix	773-774	2
β-strand	775	1	39
β-strand	781-790	10	36
β-strand	792	1	36
β-strand	793-795	3	35
β-strand	798	1	37
β-strand	805-814	10	36
β-strand	818-821	4	36
α-helix	822-824	3
β-strand	825-829	5	36
β-strand	833-836	4	40
β-strand	843	1	41
β-strand	850-851	2	42
β-strand	854-857	4	40
β-strand	863-869	7	39
β-strand	884-889	6	39
β-strand	893-896	4	40
β-strand	899-900	2	42
β-strand	909-916	8	39
β-strand	918	1	38
β-strand	924-931	8	39
β-strand	933	1	41
α-helix	934-935	2
β-strand	938-948	11	27
β-strand	960	1	43
β-strand	974-982	9	27
α-helix	983-985	3
α-helix	1001-1003	3
α-helix	1013-1025	13
α-helix	1041-1059	19
α-helix	1076-1084	9
α-helix	1100-1109	10
α-helix	1138-1151	14
α-helix	1165-1185	21
α-helix	1190-1202	13
α-helix	1207-1219	13
α-helix	1262-1275	14
α-helix	1280-1291	12
α-helix	1292-1294	3
α-helix	1302-1319	18
β-strand	1327-1334	8	43
β-strand	1339-1346	8	43
β-strand	1353-1357	5	27
β-strand	1366-1371	6	43
β-strand	1376-1386	11	27
β-strand	1397-1405	9	44
β-strand	1409	1	45
β-strand	1464-1474	11	44
β-strand	1484-1489	6	46
β-strand	1494-1496	3	44
α-helix	1498-1505	8
β-strand	1515-1518	4	46
β-strand	1521-1526	6	46
β-strand	1534-1542	9	44
α-helix	1545	1
β-strand	1546	1	45
β-strand	1552-1558	7	46
β-strand	1565-1570	6	46
α-helix	1571-1572	2
β-strand	1581-1584	4	47
β-strand	1587-1590	4	47
α-helix	1594-1596	3
α-helix	1612-1618	7
β-strand	1625-1637	13	48
β-strand	1640-1652	13	48
β-strand	1664-1670	7	48
β-strand	1682-1687	6	48
β-strand	1693	1	49
β-strand	1699	1	49
β-strand	1701-1702	2	48
β-strand	1708-1711	4	48
α-helix	1712-1714	3
α-helix	1715-1719	5
α-helix	1721-1724	4
α-helix	1727-1739	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine protease complement C2b	B	protein	509	Homo sapiens	P06681 (AlphaFold model)
Complement C3	C, D	protein	1663	Homo sapiens	P01024 (AlphaFold model)
Complement C4-B	E	protein	1744	Homo sapiens	P0C0L5 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9U61_1 Serine protease complement C2b (chains B)
KIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFASEPK
VLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMA
WQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDWREL
NELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPWHVT
IKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVISPG
FDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTCRDH
ENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVTDQF
LCSGTQEDESPCKGESGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRSKVP
PPRDFHINLFRMQPWLRQHLGDVLNFLPL

Sequence of entity 2 (C, D), FASTA

>9U61_2 Complement C3 (chains C, D)
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 3 (E), FASTA

>9U61_3 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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
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
9U5Z 3.1 Å, C3 convertases zymogen C4b2 in activation state
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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