9QO3: COP9 signalosome complex subunit 1

Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex. Determined by electron microscopy at 4.6 Å resolution. Released 18 Feb 2026.

Method
Electron microscopy
Resolution
4.6 Å
Organism
Homo sapiens
Chains
13
Atoms
28,850
Mol. weight
501.16 kDa
Ligands
IHP, ZN
Released
18 Feb 2026

Explore 9QO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QO3 contains 192 α-helices and 84 β-strands across 13 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: 24 helices, 5 β-strands

ElementResiduesLengthSheet
α-helix44-474
β-strand5211
α-helix54-6512
α-helix71-8212
α-helix88-10417
α-helix129-15527
α-helix158-17518
α-helix178-1869
α-helix195-21218
α-helix215-22713
α-helix241-25919
α-helix264-2707
α-helix285-2895
α-helix290-30011
α-helix303-3064
α-helix307-3115
α-helix314-3218
α-helix324-33411
α-helix338-35215
α-helix359-3613
α-helix362-37817
β-strand383-38532
α-helix386-3927
α-helix397-41014
β-strand415-41842
β-strand423-42642
α-helix431-46232
β-strand46613
α-helix467-4682
Chain B: 25 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix36-427
α-helix52-609
α-helix66-8116
α-helix85-884
α-helix89-935
α-helix94-952
α-helix96-1005
α-helix105-12319
α-helix126-1283
α-helix146-16116
α-helix166-1716
α-helix176-1805
β-strand181-182221
β-strand185-186221
α-helix194-20815
α-helix212-22110
α-helix231-24818
α-helix253-26816
α-helix273-28614
α-helix297-2993
α-helix301-3033
α-helix309-32012
α-helix324-3329
α-helix347-36317
β-strand366-37052
α-helix371-3788
α-helix382-39413
β-strand401-40332
β-strand408-41032
α-helix420-44122
Chain C: 26 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix5-1511
α-helix21-3010
α-helix33-364
α-helix57-659
α-helix74-8613
α-helix90-945
α-helix99-11416
α-helix120-12910
β-strand13814
α-helix141-15111
α-helix159-1613
β-strand16914
α-helix172-1743
α-helix178-19417
α-helix198-20912
β-strand21313
β-strand21615
α-helix218-23518
α-helix239-2424
α-helix247-2482
α-helix249-2535
α-helix254-2563
α-helix258-26811
α-helix272-28110
α-helix283-2886
α-helix294-31017
β-strand314-31852
α-helix319-3257
α-helix331-34414
β-strand349-35242
β-strand357-36042
α-helix370-39728
α-helix401-4077
Chain D: 21 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix40-5314
α-helix61-7212
α-helix78-8912
α-helix101-11616
α-helix120-1278
α-helix143-15816
α-helix161-17515
α-helix181-19717
α-helix203-21210
α-helix219-23517
α-helix2371
α-helix240-25112
α-helix255-2573
α-helix261-2699
α-helix275-2839
α-helix288-2903
β-strand29216
β-strand29816
α-helix299-31517
β-strand316-32052
α-helix321-3288
α-helix332-34413
β-strand350-35342
β-strand358-36142
α-helix366-38924
α-helix393-40412
Chain E: 14 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix26-283
α-helix33-419
α-helix44-485
β-strand54-5747
α-helix59-7113
β-strand79-8138
β-strand8517
β-strand91-9227
β-strand95-9738
α-helix109-12416
β-strand135-13848
α-helix149-15911
β-strand166-17058
α-helix172-1787
β-strand183-18868
α-helix208-2103
α-helix211-2166
β-strand221-22448
β-strand225-22847
α-helix232-24110
α-helix242-2443
α-helix246-2516
α-helix259-28022
α-helix299-32830
Chain F: 7 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand3119
β-strand40-4239
α-helix45-6117
β-strand70-7569
β-strand80-8899
β-strand91-93310
β-strand98-100310
α-helix102-11211
β-strand120-12789
α-helix133-14311
β-strand150-15459
β-strand165-174109
β-strand179-18689
β-strand18919
α-helix194-20411
α-helix216-24732
α-helix254-26613
α-helix273-31240
Chain G: 13 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix11-188
α-helix26-3611
α-helix44-474
α-helix50-534
α-helix54-563
α-helix61-7212
α-helix75-806
α-helix86-894
α-helix90-10718
β-strand110-11232
α-helix113-1208
α-helix125-13814
β-strand141-14662
β-strand151-15772
α-helix164-1663
α-helix167-22458
Chain H: 10 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix12-2514
α-helix34-4613
α-helix50-5910
α-helix62-654
α-helix70-8314
α-helix86-938
α-helix103-12422
β-strand125-12732
β-strand128-129211
α-helix130-1378
α-helix141-15010
β-strand154-156311
β-strand161-163311
α-helix196-20712

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
COP9 signalosome complex subunit 1Aprotein491Homo sapiensQ13098 (AlphaFold model)
COP9 signalosome complex subunit 3Cprotein423Homo sapiensQ9UNS2 (AlphaFold model)
COP9 signalosome complex subunit 4Dprotein406Homo sapiensQ9BT78 (AlphaFold model)
COP9 signalosome complex subunit 5Eprotein334Homo sapiensQ92905 (AlphaFold model)
COP9 signalosome complex subunit 6Fprotein327Homo sapiensQ7L5N1
COP9 signalosome complex subunit 7bGprotein264Homo sapiensQ9H9Q2
COP9 signalosome complex subunit 8Hprotein209Homo sapiensQ99627
Cullin-1Iprotein776Homo sapiensQ13616
S-phase kinase-associated protein 1Lprotein163Homo sapiensP63208
S-phase kinase-associated protein 2Mprotein424Homo sapiensQ13309
Cyclin-dependent kinases regulatory subunit 1Nprotein79Homo sapiensP61024
COP9 signalosome complex subunit 2Bprotein443Homo sapiensP61201

1 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>9QO3_1 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 2 (C), FASTA
>9QO3_2 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 3 (D), FASTA
>9QO3_3 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 4 (E), FASTA
>9QO3_4 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 5 (F), FASTA
>9QO3_5 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 6 (G), FASTA
>9QO3_6 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 7 (H), FASTA
>9QO3_7 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 8 (I), FASTA
>9QO3_8 Cullin-1 (chains I)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 9 (L), FASTA
>9QO3_9 S-phase kinase-associated protein 1 (chains L)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 10 (M), FASTA
>9QO3_10 S-phase kinase-associated protein 2 (chains M)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL
Sequence of entity 11 (N), FASTA
>9QO3_11 Cyclin-dependent kinases regulatory subunit 1 (chains N)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK
Sequence of entity 12 (B), FASTA
>9QO3_12 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P61
ZNZinc ionZn1

Primary citation

Structural basis of CSN-mediated SCF deneddylation. Ding, S., Clapperton, J.A., Maeots, M.E. et al. Nat Commun (2026) 17:951-951. DOI 10.1038/s41467-025-67566-y · PubMed

Other PDB entries of the same protein (UniProt Q13098 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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