9QO6: 9-subunit COP9 signalosome complex
9-subunit COP9 signalosome complex. Determined by electron microscopy at 3.0 Å resolution. Released 4 Feb 2026.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 9
- Atoms
- 17,380
- Mol. weight
- 334.47 kDa
- Ligands
- ZN
- Released
- 4 Feb 2026
Explore 9QO6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9QO6 contains 113 α-helices and 48 β-strands across 9 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: 21 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 54-65 | 12 | |
| α-helix | 68-71 | 4 | |
| α-helix | 73-82 | 10 | |
| α-helix | 89-102 | 14 | |
| α-helix | 129-155 | 27 | |
| α-helix | 158-174 | 17 | |
| α-helix | 178-186 | 9 | |
| α-helix | 195-211 | 17 | |
| α-helix | 215-226 | 12 | |
| α-helix | 247-259 | 13 | |
| α-helix | 263-270 | 8 | |
| α-helix | 286-298 | 13 | |
| α-helix | 303-306 | 4 | |
| α-helix | 307-311 | 5 | |
| α-helix | 314-322 | 9 | |
| α-helix | 324-334 | 11 | |
| α-helix | 341-345 | 5 | |
| α-helix | 362-378 | 17 | |
| β-strand | 381-385 | 5 | 2 |
| α-helix | 386-391 | 6 | |
| α-helix | 397-409 | 13 | |
| β-strand | 415-418 | 4 | 2 |
| β-strand | 423-426 | 4 | 2 |
| α-helix | 431-462 | 32 | |
| β-strand | 466 | 1 | 3 |
Chain B: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 310-320 | 11 | |
| α-helix | 323-332 | 10 | |
| α-helix | 335-338 | 4 | |
| α-helix | 341-362 | 22 | |
| β-strand | 366-370 | 5 | 2 |
| α-helix | 371-378 | 8 | |
| α-helix | 382-394 | 13 | |
| β-strand | 400-403 | 4 | 2 |
| β-strand | 408-411 | 4 | 2 |
| α-helix | 419-440 | 22 | |
Chain C: 26 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| α-helix | 23-30 | 8 | |
| α-helix | 33-36 | 4 | |
| α-helix | 39-41 | 3 | |
| α-helix | 42-48 | 7 | |
| α-helix | 57-65 | 9 | |
| α-helix | 74-86 | 13 | |
| α-helix | 90-93 | 4 | |
| α-helix | 99-113 | 15 | |
| α-helix | 117-119 | 3 | |
| α-helix | 120-129 | 10 | |
| β-strand | 137-138 | 2 | 4 |
| α-helix | 142-151 | 10 | |
| α-helix | 159-161 | 3 | |
| β-strand | 168-169 | 2 | 4 |
| α-helix | 178-194 | 17 | |
| α-helix | 198-210 | 13 | |
| β-strand | 213 | 1 | 3 |
| β-strand | 217 | 1 | 5 |
| α-helix | 218-234 | 17 | |
| α-helix | 238-242 | 5 | |
| α-helix | 254-256 | 3 | |
| α-helix | 258-268 | 11 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 295-310 | 16 | |
| β-strand | 314-318 | 5 | 2 |
| α-helix | 321-325 | 5 | |
| α-helix | 330-344 | 15 | |
| β-strand | 349-352 | 4 | 2 |
| β-strand | 357-360 | 4 | 2 |
| α-helix | 372-398 | 27 | |
| α-helix | 401-408 | 8 | |
Chain D: 16 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 142-157 | 16 | |
| α-helix | 161-171 | 11 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-212 | 12 | |
| α-helix | 219-235 | 17 | |
| α-helix | 237 | 1 | |
| α-helix | 240-251 | 12 | |
| α-helix | 255-257 | 3 | |
| α-helix | 261-269 | 9 | |
| α-helix | 275-282 | 8 | |
| α-helix | 287-289 | 3 | |
| β-strand | 292 | 1 | 6 |
| β-strand | 298 | 1 | 6 |
| α-helix | 299-312 | 14 | |
| β-strand | 316-320 | 5 | 2 |
| α-helix | 321-328 | 8 | |
| α-helix | 332-345 | 14 | |
| β-strand | 350-353 | 4 | 2 |
| β-strand | 358-361 | 4 | 2 |
| 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 | 1 |
| α-helix | 59-71 | 13 | |
| β-strand | 78-86 | 9 | 1 |
| β-strand | 89-97 | 9 | 1 |
| α-helix | 109-124 | 16 | |
| β-strand | 135-139 | 5 | 1 |
| α-helix | 149-159 | 11 | |
| β-strand | 166-170 | 5 | 1 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-188 | 6 | 1 |
| 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 | 1 |
| 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, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31 | 1 | 7 |
| β-strand | 40-43 | 4 | 7 |
| α-helix | 45-62 | 18 | |
| β-strand | 69 | 1 | 7 |
| β-strand | 70 | 1 | 8 |
| β-strand | 72-77 | 6 | 7 |
| β-strand | 80-85 | 6 | 7 |
| β-strand | 88 | 1 | 8 |
| β-strand | 91-94 | 4 | 9 |
| β-strand | 97-100 | 4 | 9 |
| α-helix | 102-115 | 14 | |
| β-strand | 120-127 | 8 | 7 |
| α-helix | 133-143 | 11 | |
| β-strand | 150-154 | 5 | 7 |
| β-strand | 165-175 | 11 | 7 |
| β-strand | 178-185 | 8 | 7 |
| β-strand | 188-190 | 3 | 7 |
| α-helix | 194-205 | 12 | |
| α-helix | 216-247 | 32 | |
| α-helix | 255-264 | 10 | |
| α-helix | 273-312 | 40 | |
Chain G: 10 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-18 | 8 | |
| α-helix | 27-36 | 10 | |
| α-helix | 46-48 | 3 | |
| α-helix | 50-53 | 4 | |
| α-helix | 61-72 | 12 | |
| α-helix | 75-80 | 6 | |
| α-helix | 90-105 | 16 | |
| β-strand | 110-112 | 3 | 2 |
| α-helix | 113-120 | 8 | |
| α-helix | 125-137 | 13 | |
| β-strand | 141-146 | 6 | 2 |
| β-strand | 151-157 | 7 | 2 |
| α-helix | 167-221 | 55 | |
Chain H: 10 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 | 62-67 | 6 | |
| α-helix | 70-82 | 13 | |
| α-helix | 86-93 | 8 | |
| α-helix | 103-123 | 21 | |
| β-strand | 127 | 1 | 2 |
| β-strand | 128-129 | 2 | 10 |
| α-helix | 130-137 | 8 | |
| α-helix | 141-151 | 11 | |
| β-strand | 154-156 | 3 | 10 |
| β-strand | 161-163 | 3 | 10 |
| α-helix | 197-208 | 12 | |
1 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 5 | E | protein | 334 | Homo sapiens | Q92905 (AlphaFold model) |
| 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 |
| 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 |
| COP9 signalosome complex subunit 9 | P | protein | 57 | Homo sapiens | Q8WXC6 |
Sequence of entity 1 (E), FASTA
>9QO6_1 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTATRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 2 (A), FASTA
>9QO6_2 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 3 (B), FASTA
>9QO6_3 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 4 (C), FASTA
>9QO6_4 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 5 (D), FASTA
>9QO6_5 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 6 (F), FASTA
>9QO6_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>9QO6_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 8 (H), FASTA
>9QO6_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (P), FASTA
>9QO6_9 COP9 signalosome complex subunit 9 (chains P)
MKPAVDEMFPEGAGPYVDLDEAGGSTGLLMDLAANEKAVHADFFNDFEDLFDDDDIQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 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 Q92905 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5JOH 1.99 Å, Crystal structure of CSN5(2-257) in complex with CNS5i-1b
- 5M5Q 2.2 Å, COPS5(2-257) in complex with a azaindole (compound 4)
- 5JOG 2.46 Å, Crystal structure of CSN5(2-257) in complex with CNS5i-3
- 4F7O 2.6 Å, Crystal structure of CSN5
- 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
- 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
Browse structure collections
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