9QO5: COP9 signalosome complex subunit 1
Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex. Determined by electron microscopy at 4.0 Å resolution. Released 4 Feb 2026.
- Method
- Electron microscopy
- Resolution
- 4.0 Å
- Organism
- Homo sapiens
- Chains
- 14
- Atoms
- 29,818
- Mol. weight
- 513.39 kDa
- Ligands
- IHP, ZN
- Released
- 4 Feb 2026
Explore 9QO5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9QO5 contains 207 α-helices and 75 β-strands across 12 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, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-47 | 4 | |
| α-helix | 54-65 | 12 | |
| α-helix | 71-81 | 11 | |
| α-helix | 88-104 | 17 | |
| α-helix | 129-147 | 19 | |
| α-helix | 149-155 | 7 | |
| α-helix | 158-175 | 18 | |
| α-helix | 178-186 | 9 | |
| α-helix | 195-212 | 18 | |
| α-helix | 215-227 | 13 | |
| α-helix | 241-259 | 19 | |
| α-helix | 263-270 | 8 | |
| α-helix | 285-289 | 5 | |
| α-helix | 290-297 | 8 | |
| α-helix | 305-306 | 2 | |
| α-helix | 307-311 | 5 | |
| α-helix | 317-321 | 5 | |
| α-helix | 324-333 | 10 | |
| α-helix | 338-352 | 15 | |
| α-helix | 359-361 | 3 | |
| α-helix | 362-378 | 17 | |
| β-strand | 383-385 | 3 | 1 |
| α-helix | 386-392 | 7 | |
| α-helix | 397-410 | 14 | |
| β-strand | 415-418 | 4 | 1 |
| β-strand | 423-426 | 4 | 1 |
| α-helix | 431-462 | 32 | |
| β-strand | 466 | 1 | 2 |
Chain B: 20 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-40 | 6 | |
| α-helix | 47-59 | 13 | |
| α-helix | 67-80 | 14 | |
| α-helix | 85-98 | 14 | |
| α-helix | 105-120 | 16 | |
| α-helix | 127-141 | 15 | |
| α-helix | 145-161 | 17 | |
| α-helix | 168-178 | 11 | |
| α-helix | 191-207 | 17 | |
| α-helix | 212-221 | 10 | |
| α-helix | 231-247 | 17 | |
| α-helix | 251-268 | 18 | |
| α-helix | 273-287 | 15 | |
| α-helix | 300-302 | 3 | |
| α-helix | 306-319 | 14 | |
| α-helix | 323-332 | 10 | |
| α-helix | 341-363 | 23 | |
| β-strand | 366-370 | 5 | 1 |
| α-helix | 371-378 | 8 | |
| α-helix | 382-394 | 13 | |
| β-strand | 400-403 | 4 | 1 |
| β-strand | 408-411 | 4 | 1 |
| α-helix | 419-440 | 22 | |
Chain C: 28 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 21-30 | 10 | |
| α-helix | 35-37 | 3 | |
| α-helix | 57-65 | 9 | |
| α-helix | 74-86 | 13 | |
| α-helix | 90-93 | 4 | |
| α-helix | 99-113 | 15 | |
| α-helix | 117-120 | 4 | |
| α-helix | 121-131 | 11 | |
| β-strand | 138 | 1 | 3 |
| α-helix | 142-151 | 10 | |
| α-helix | 159-162 | 4 | |
| β-strand | 169 | 1 | 3 |
| α-helix | 172-174 | 3 | |
| α-helix | 178-194 | 17 | |
| α-helix | 198-210 | 13 | |
| β-strand | 213 | 1 | 2 |
| α-helix | 218-234 | 17 | |
| α-helix | 238-242 | 5 | |
| α-helix | 248 | 1 | |
| α-helix | 249-253 | 5 | |
| α-helix | 254-257 | 4 | |
| α-helix | 258-268 | 11 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-309 | 16 | |
| α-helix | 310-312 | 3 | |
| β-strand | 314-318 | 5 | 1 |
| α-helix | 319-326 | 8 | |
| α-helix | 331-343 | 13 | |
| β-strand | 349-352 | 4 | 1 |
| β-strand | 357-360 | 4 | 1 |
| α-helix | 373-398 | 26 | |
| α-helix | 401-407 | 7 | |
Chain D: 24 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-52 | 11 | |
| α-helix | 63-71 | 9 | |
| α-helix | 78-88 | 11 | |
| α-helix | 93-95 | 3 | |
| α-helix | 102-117 | 16 | |
| α-helix | 125-128 | 4 | |
| α-helix | 141-158 | 18 | |
| α-helix | 161-170 | 10 | |
| α-helix | 182-197 | 16 | |
| α-helix | 203-211 | 9 | |
| α-helix | 219-235 | 17 | |
| α-helix | 237 | 1 | |
| α-helix | 240-251 | 12 | |
| α-helix | 254-257 | 4 | |
| α-helix | 261-269 | 9 | |
| α-helix | 275-282 | 8 | |
| α-helix | 287-289 | 3 | |
| α-helix | 291 | 1 | |
| β-strand | 292 | 1 | 4 |
| α-helix | 293 | 1 | |
| β-strand | 298 | 1 | 4 |
| α-helix | 299-315 | 17 | |
| β-strand | 316-320 | 5 | 1 |
| α-helix | 321-328 | 8 | |
| α-helix | 332-344 | 13 | |
| β-strand | 350-353 | 4 | 1 |
| β-strand | 358-361 | 4 | 1 |
| α-helix | 366-391 | 26 | |
| α-helix | 393-405 | 13 | |
Chain E: 16 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 33-41 | 9 | |
| α-helix | 45-48 | 4 | |
| β-strand | 54-58 | 5 | 17 |
| α-helix | 59-71 | 13 | |
| β-strand | 78-86 | 9 | 17 |
| β-strand | 89-97 | 9 | 17 |
| α-helix | 109-124 | 16 | |
| β-strand | 135-139 | 5 | 17 |
| α-helix | 149-159 | 11 | |
| β-strand | 166-170 | 5 | 17 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-188 | 6 | 17 |
| α-helix | 189-190 | 2 | |
| α-helix | 196-198 | 3 | |
| α-helix | 211-216 | 6 | |
| α-helix | 217-219 | 3 | |
| β-strand | 221-229 | 9 | 17 |
| α-helix | 232-239 | 8 | |
| α-helix | 242-244 | 3 | |
| α-helix | 246-250 | 5 | |
| α-helix | 259-280 | 22 | |
| α-helix | 299-328 | 30 | |
Chain F: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31 | 1 | 5 |
| β-strand | 40-43 | 4 | 5 |
| α-helix | 45-61 | 17 | |
| β-strand | 69-75 | 7 | 5 |
| β-strand | 80-88 | 9 | 5 |
| β-strand | 92-93 | 2 | 6 |
| β-strand | 98-99 | 2 | 6 |
| α-helix | 102-115 | 14 | |
| β-strand | 120-127 | 8 | 5 |
| α-helix | 133-143 | 11 | |
| β-strand | 150-154 | 5 | 5 |
| β-strand | 165-175 | 11 | 5 |
| β-strand | 178-186 | 9 | 5 |
| β-strand | 188-190 | 3 | 5 |
| α-helix | 194-204 | 11 | |
| α-helix | 216-247 | 32 | |
| α-helix | 254-266 | 13 | |
| α-helix | 273-312 | 40 | |
Chain G: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 26-36 | 11 | |
| α-helix | 44-48 | 5 | |
| α-helix | 50-53 | 4 | |
| α-helix | 61-72 | 12 | |
| α-helix | 75-80 | 6 | |
| α-helix | 82-84 | 3 | |
| α-helix | 86-88 | 3 | |
| α-helix | 90-105 | 16 | |
| β-strand | 110-112 | 3 | 1 |
| α-helix | 113-120 | 8 | |
| α-helix | 125-137 | 13 | |
| β-strand | 141-146 | 6 | 1 |
| β-strand | 151-157 | 7 | 1 |
| α-helix | 167-224 | 58 | |
Chain H: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-25 | 14 | |
| α-helix | 34-47 | 14 | |
| α-helix | 50-59 | 10 | |
| α-helix | 62-65 | 4 | |
| α-helix | 70-82 | 13 | |
| α-helix | 86-93 | 8 | |
| α-helix | 100-102 | 3 | |
| α-helix | 103-123 | 21 | |
| β-strand | 125-127 | 3 | 1 |
| β-strand | 128-129 | 2 | 7 |
| α-helix | 130-137 | 8 | |
| α-helix | 141-150 | 10 | |
| β-strand | 154-156 | 3 | 7 |
| β-strand | 161-163 | 3 | 7 |
| α-helix | 196-207 | 12 | |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| COP9 signalosome complex subunit 1 | A | protein | 491 | Homo sapiens | Q13098 (AlphaFold model) |
| COP9 signalosome complex subunit 2 | B | protein | 443 | Homo sapiens | P61201 (AlphaFold model) |
| COP9 signalosome complex subunit 3 | C | protein | 423 | Homo sapiens | Q9UNS2 (AlphaFold model) |
| COP9 signalosome complex subunit 4 | D | protein | 406 | Homo sapiens | Q9BT78 (AlphaFold model) |
| COP9 signalosome complex subunit 6 | F | protein | 327 | Homo sapiens | Q7L5N1 |
| COP9 signalosome complex subunit 7b | G | protein | 264 | Homo sapiens | Q9H9Q2 |
| COP9 signalosome complex subunit 8 | H | protein | 209 | Homo sapiens | Q99627 |
| Cullin-1 | I | protein | 776 | Homo sapiens | Q13616 |
| E3 ubiquitin-protein ligase RBX1 | J | protein | 108 | Homo sapiens | P62877 |
| S-phase kinase-associated protein 1 | L | protein | 163 | Homo sapiens | P63208 |
| S-phase kinase-associated protein 2 | M | protein | 424 | Homo sapiens | Q13309 |
| Cyclin-dependent kinases regulatory subunit 1 | N | protein | 79 | Homo sapiens | P61024 |
2 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>9QO5_1 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>9QO5_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>9QO5_3 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 4 (D), FASTA
>9QO5_4 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (F), FASTA
>9QO5_5 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 6 (G), FASTA
>9QO5_6 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 7 (H), FASTA
>9QO5_7 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 8 (I), FASTA
>9QO5_8 Cullin-1 (chains I)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 9 (J), FASTA
>9QO5_9 E3 ubiquitin-protein ligase RBX1 (chains J)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 10 (L), FASTA
>9QO5_10 S-phase kinase-associated protein 1 (chains L)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 11 (M), FASTA
>9QO5_11 S-phase kinase-associated protein 2 (chains M)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL
Sequence of entity 12 (N), FASTA
>9QO5_12 Cyclin-dependent kinases regulatory subunit 1 (chains N)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| IHP | Inositol hexakisphosphate | C6 H18 O24 P6 | 1 |
| ZN | Zinc ion | Zn | 1 |
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:
- 9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
- 9EFQ 2.96 Å, Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2
- 9PH4 3.0 Å, Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a
- 9QO6 3.0 Å, 9-subunit COP9 signalosome complex
- 9EFV 3.03 Å, Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3
- 9EFM 3.16 Å, Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1
- 9QO1 3.23 Å, Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure
- 9QO0 3.26 Å, Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex…
- 9E77 3.3 Å, Cryo-EM structure of CSN-N8 in complex with CSN5i-3
- 9E81 3.3 Å, Cryo-EM structure of COP9 signalosome in complex with CSN5i-3
- 9EG8 3.39 Å, Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A
- 9E5Z 3.4 Å, Cryo-EM structure of COP9 signalosome
Browse structure collections
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