9QK2: Complement C4-A

Structure of the Complement classical and lectin pathway C3 convertase in complex with substrate C3. Determined by electron microscopy at 3.5 Å resolution. Released 24 Dec 2025.

Method
Electron microscopy
Resolution
3.5 Å
Organisms
Homo sapiens, Lama glama
Chains
7
Atoms
29,917
Mol. weight
1052.22 kDa
Ligands
MG, NAG
Released
24 Dec 2025

Explore 9QK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QK2 contains 112 α-helices and 266 β-strands across 7 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: 15 helices, 53 β-strands

ElementResiduesLengthSheet
β-strand22-2651
β-strand30-3232
β-strand37-4481
β-strand52-5983
β-strand72-7653
β-strand82-8761
α-helix91-966
α-helix99-1013
β-strand109-11353
α-helix115-1162
α-helix117-1215
β-strand127-13153
β-strand133-13532
β-strand140-14564
β-strand149-15025
β-strand155-16394
β-strand16914
β-strand174-17965
β-strand185-18845
β-strand197-20374
α-helix208-2092
β-strand211-21995
β-strand227-23375
β-strand241-24776
β-strand251-25337
β-strand262-27096
β-strand27516
β-strand278-287107
β-strand293-29537
β-strand301-30447
β-strand30616
β-strand309-31466
α-helix316-32510
α-helix330-3323
β-strand337-346107
β-strand352-35767
β-strand361-36337
β-strand367-36828
α-helix378-3792
β-strand384-38969
β-strand391-39228
β-strand39718
α-helix3981
β-strand402-409810
β-strand417-424810
β-strand430-43569
β-strand443-450810
β-strand456-463810
α-helix464-4663
β-strand472-476511
β-strand488-496911
β-strand504-511812
β-strand514-522912
β-strand527-532611
β-strand540-548912
β-strand553-556412
β-strand559-561312
α-helix562-5643
β-strand574113
β-strand586-591613
β-strand596-600514
β-strand601-604415
α-helix607-6115
α-helix621-6299
α-helix643-6508
β-strand655116
β-strand660116
α-helix661-6644
Chain B: 19 helices, 35 β-strands
ElementResiduesLengthSheet
β-strand766131
α-helix7731
β-strand774-775232
β-strand781-782215
β-strand786-790514
β-strand793-798613
β-strand805-810615
β-strand813-814214
β-strand818-819214
β-strand825-828415
β-strand833-836433
β-strand843-844234
β-strand849-851335
β-strand854-857433
β-strand865-869532
β-strand875-876236
β-strand885-887332
β-strand893-896433
β-strand899-901335
β-strand902-903236
β-strand908-9171032
β-strand918131
β-strand924-932932
β-strand933-934234
α-helix9351
β-strand938-948115
α-helix954-9563
β-strand957-960437
β-strand96815
β-strand975-98175
α-helix982-9832
α-helix997-10015
α-helix1013-103119
α-helix1034-10363
α-helix1039-105517
α-helix1056-10583
α-helix1076-108813
α-helix1097-110913
α-helix1127-11326
α-helix1138-115417
α-helix1162-118524
α-helix1190-120213
α-helix1207-121913
α-helix1259-127416
α-helix1282-129312
α-helix1302-131918
β-strand1327-1334837
β-strand1339-1344637
β-strand1355-136065
β-strand1366-1372737
β-strand1376-1386115
β-strand1397-1401518
β-strand1404-1405217
β-strand1409120
Chain C: 4 helices, 23 β-strands
ElementResiduesLengthSheet
β-strand1465-1467317
β-strand1470-1474518
β-strand1484-1489619
β-strand1494-1496317
α-helix1498-15058
β-strand1514-1518519
β-strand1521-1526619
β-strand1535-1536218
β-strand1539-1542417
β-strand1546120
β-strand1552-1558719
β-strand1565-1570619
β-strand1581121
β-strand1584122
β-strand1587122
β-strand1590121
α-helix1614-16185
β-strand1625-16371323
β-strand1640-16521323
β-strand1663-1670823
β-strand1682-1687623
β-strand1692-1693224
β-strand1699-1700224
β-strand1701-1702223
β-strand1708-1711423
α-helix1712-17132
α-helix1721-173919
Chain D: 1 helix, 11 β-strands
ElementResiduesLengthSheet
β-strand4-7438
β-strand13139
β-strand19-24638
β-strand31-35540
β-strand42-47640
β-strand54-56340
α-helix58-603
β-strand65-68438
β-strand74-78538
β-strand88-93640
β-strand114-116340
β-strand119139
Chain E: 16 helices, 25 β-strands
ElementResiduesLengthSheet
β-strand245-246225
β-strand252-260926
α-helix267-28620
β-strand291-298826
β-strand302-306526
α-helix311-3144
α-helix316-3249
α-helix329-3313
α-helix339-35517
α-helix362-3654
β-strand367-374826
α-helix385-39511
α-helix403-4053
β-strand406-412726
α-helix420-4267
β-strand436-438326
α-helix442-45110
β-strand453-454225
α-helix474-4774
β-strand481-485527
β-strand492-496527
β-strand501-504427
β-strand519-522427
β-strand531-5401027
β-strand563-567527
β-strand574128
β-strand577128
β-strand581129
β-strand585130
α-helix586-5916
α-helix600-6078
β-strand612-618729
β-strand624-630729
α-helix633-64412
β-strand663-664229
β-strand682-687629
β-strand690-6991029
β-strand728-730329
α-helix733-7353
α-helix736-7438
β-strand749130
Chain F: 15 helices, 62 β-strands
ElementResiduesLengthSheet
β-strand25-31741
β-strand33-34242
β-strand36143
β-strand39-47941
β-strand53-61942
β-strand68-76942
α-helix78-803
β-strand83-89741
β-strand90143
β-strand105-112842
β-strand115-123942
β-strand129-134644
β-strand138145
α-helix1431
β-strand144-152944
β-strand158144
β-strand162-168745
β-strand174-181845
β-strand188-194744
β-strand203-210845
β-strand218-223645
β-strand232-238746
β-strand243-244247
β-strand251-259946
β-strand264146
β-strand267-2761048
β-strand277149
β-strand280149
β-strand283148
β-strand289-293548
β-strand294146
β-strand297146
β-strand300-302346
α-helix304-3107
α-helix316-3194
β-strand323-3321048
β-strand338-346948
β-strand348-349247
β-strand354-357450
β-strand363-364251
β-strand370-371252
β-strand374-377450
β-strand383150
β-strand388-391453
β-strand399-400253
β-strand406-407250
β-strand410-411252
α-helix412-4143
α-helix4191
β-strand420-426753
α-helix433-4353
β-strand438-443653
β-strand444-445251
β-strand455-459554
β-strand465155
β-strand470-478954
α-helix484-4863
β-strand489-490256
β-strand491-496657
β-strand499-503557
β-strand506-507256
β-strand514-520754
α-helix523-5253
β-strand529-5381057
β-strand544-5531057
β-strand555155
β-strand563-567558
β-strand580-588958
β-strand592-598759
α-helix601-6055
α-helix606-6083
α-helix613-6219
α-helix635-6417
β-strand644-648541
β-strand653141
α-helix654-6563
α-helix662-6643
Chain G: 42 helices, 57 β-strands
ElementResiduesLengthSheet
α-helix676-6838
α-helix688-69811
α-helix700-7012
α-helix707-7104
α-helix711-7133
α-helix718-74124
α-helix750-7523
α-helix768-7703
β-strand771159
β-strand775-777359
α-helix781-7822
β-strand783158
β-strand786-794958
β-strand801-8101059
β-strand814-817459
α-helix818-8203
β-strand821-824459
β-strand829-834660
β-strand838-840361
β-strand844-845262
β-strand848-853660
β-strand860-866761
β-strand869163
β-strand872163
β-strand882-888761
α-helix8891
β-strand892-897660
β-strand900162
β-strand902163
β-strand906-9161161
β-strand924-932961
β-strand936-943864
β-strand946-947264
β-strand958-962565
α-helix963-9653
β-strand970164
α-helix9711
β-strand977-983764
α-helix988-9958
α-helix1000-10034
α-helix1013-10153
α-helix1019-103113
α-helix1034-10374
α-helix1040-105617
α-helix1057-10593
β-strand1060166
β-strand1066166
β-strand1067167
β-strand1074167
α-helix1076-108712
α-helix1097-111014
β-strand1112168
β-strand1118168
α-helix1123-11242
α-helix1140-115314
α-helix1165-117814
α-helix1180-11823
α-helix1186-119914
α-helix1205-12139
β-strand1215169
β-strand1219169
α-helix1227-124216
α-helix1249-12568
β-strand1262170
β-strand1265170
α-helix1269-128416
β-strand1293-1299765
α-helix13061
β-strand1307-1312665
β-strand1319-1324664
β-strand1330-1334565
β-strand1340-13501164
β-strand1361-1369971
β-strand1382-13921171
β-strand1401-1406672
β-strand1411-1413371
α-helix1415-14239
β-strand1431-1433372
β-strand1443-1448672
β-strand1457-1465971
β-strand1469-1470262
α-helix1472-14743
β-strand1475-1481772
β-strand1488-1493672
α-helix1510-15156
α-helix1529-15368
β-strand1541-15531373
β-strand1558-15701373
β-strand1581-1587773
α-helix1588-15903
α-helix1591-15944
β-strand1601-1607773
β-strand1611173
β-strand1620-1621273
β-strand1629-1631373
α-helix1632-16332
α-helix1635-16384
α-helix1640-165415
α-helix1655-16595

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Complement C4-AA, B, Cprotein1744Homo sapiensP0C0L4 (AlphaFold model)
Complement C2Eprotein752Homo sapiensP06681 (AlphaFold model)
Anti-C4b nanobody B12Dprotein120Lama glama
Complement C3F, Gprotein1663Homo sapiensP01024 (AlphaFold model)
Sequence of entity 1 (A, B, C), FASTA
>9QK2_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 (E), FASTA
>9QK2_2 Complement C2 (chains E)
MGPLMVLFCLLFLYPGLADSAPSCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPA
SRLCKSSGQWQTPGATRSLSKAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDG
FILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSN
LVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVAPALGTSFSHMLGATNPTQKTKES
LGRKIQIQRSGHLNLYLLLDCSQSVSENDFLIFKESASLMVDRIFSFEINVSVAIITFAS
EPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGME
TMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDVDW
RELNELGSKKDGERHAFILQDTKALHQVFEHMLDVSKLTDTICGVGNMSANASDQERTPW
HVTIKPKSQETCRGALISDQWVLTAAHCFRDGNDHSLWRVNVGDPKSQWGKEFLIEKAVI
SPGFDVFAKKNQGILEFYGDDIALLKLAQKVKMSTHARPICLPCTMEANLALRRPQGSTC
RDHENELLNKQSVPAHFVALNGSKLNINLKMGVEWTSCAEVVSQEKTMFPNLTDVREVVT
DQFLCSGTQEDESPCKGEAGGAVFLERRFRFFQVGLVSWGLYNPCLGSADKNSRKRAPRS
KVPPPRDFHINLFRMQPWLRQHLGDVLNFLPL
Sequence of entity 3 (D), FASTA
>9QK2_3 Anti-C4b nanobody B12 (chains D)
EVQLVESGGGLVQAGGSLRLSCVASERTYMAWFRQAPGKEREFVAAITSSGMMTEYAPSV
KGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADLRQRFGERVTEYDYWGQGTQVTVSS
Sequence of entity 4 (F, G), FASTA
>9QK2_4 Complement C3 (chains F, G)
MGPTSGPSLLLLLLTHLPLALGSPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVH
DFPGKKLVLSSEKTVLTPATNHMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKV
VLVSLQSGYLFIQTDKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSL
SSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTE
KFYYIYNEKGLEVTITARFLYGKKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEV
VLSRKVLLDGVQNLRAEDLVGKSLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKT
PKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPL
SITVRTKKQELSEAEQATRTMQALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMD
RAHEAKIRYYTYLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGA
SGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDK
GVFVLNKKNKLTQSKIWDVVEKADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAEL
QCPQPAARRRRSVQLTEKRMDKVGKYPKELRKCCEDGMRENPMRFSCQRRTRFISLGEAC
KKVFLDCCNYITELRRQHARASHLGLARSNLDEDIIAEENIVSRSEFPESWLWNVEDLKE
PPKNGISTKLMNIFLKDSITTWEILAVSMSDKKGICVADPFEVTVMQDFFIDLRLPYSVV
RNEQVEIRAVLYNYRQNQELKVRVELLHNPAFCSLATTKRRHQQTVTIPPKSSLSVPYVI
VPLKTGLQEVEVKAAVYHHFISDGVRKSLKVVPEGIRMNKTVAVRTLDPERLGREGVQKE
DIPPADLSDQVPDTESETRILLQGTPVAQMTEDAVDAERLKHLIVTPSGCGEQNMIGMTP
TVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTA
YVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKD
MALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMG
RLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQR
YYGGGYGSTQATFMVFQALAQYQKDAPDHQELNLDVSLQLPSRSSKITHRIHWESASLLR
SEETKENEGFTVTAEGKGQGTLSVVTMYHAKAKDQLTCNKFDLKVTIKPAPETEKRPQDA
KNTMILEICTRYRGDQDATMSILDISMMTGFAPDTDDLKQLANGVDRYISKYELDKAFSD
RNTLIIYLDKVSHSEDDCLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDG
KLNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDE
YIMAIEQTIKSGSDEVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSY
IIGKDTWVEHWPEEDECQDEENQKQCQDLGAFTESMVVFGCPN

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O68

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:

Browse structure collections

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