9EFQ: COP9 signalosome complex subunit 1
Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2. Determined by electron microscopy at 2.96 Å resolution. Released 3 Dec 2025.
- Method
- Electron microscopy
- Resolution
- 2.96 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 25,025
- Mol. weight
- 436.86 kDa
- Ligands
- ZN
- Released
- 3 Dec 2025
Explore 9EFQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9EFQ contains 157 α-helices and 70 β-strands across 11 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 | 44-49 | 6 | |
| α-helix | 55-65 | 11 | |
| α-helix | 71-80 | 10 | |
| α-helix | 89-100 | 12 | |
| α-helix | 128-155 | 28 | |
| α-helix | 158-175 | 18 | |
| α-helix | 179-188 | 10 | |
| α-helix | 195-212 | 18 | |
| α-helix | 215-227 | 13 | |
| α-helix | 230-233 | 4 | |
| α-helix | 245-259 | 15 | |
| α-helix | 263-270 | 8 | |
| α-helix | 275-277 | 3 | |
| α-helix | 286-300 | 15 | |
| α-helix | 303-306 | 4 | |
| α-helix | 307-311 | 5 | |
| α-helix | 315-322 | 8 | |
| α-helix | 324-334 | 11 | |
| α-helix | 339-353 | 15 | |
| α-helix | 359-361 | 3 | |
| α-helix | 362-378 | 17 | |
| β-strand | 381-385 | 5 | 1 |
| α-helix | 386-392 | 7 | |
| α-helix | 397-409 | 13 | |
| β-strand | 416-418 | 3 | 1 |
| β-strand | 423-425 | 3 | 1 |
| α-helix | 431-461 | 31 | |
| β-strand | 466 | 1 | 2 |
Chain B: 21 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-81 | 17 | |
| α-helix | 85-102 | 18 | |
| α-helix | 105-115 | 11 | |
| α-helix | 125-139 | 15 | |
| α-helix | 148-155 | 8 | |
| α-helix | 164-179 | 16 | |
| α-helix | 191-207 | 17 | |
| α-helix | 211-221 | 11 | |
| α-helix | 233-248 | 16 | |
| α-helix | 251-267 | 17 | |
| α-helix | 271-273 | 3 | |
| α-helix | 276-286 | 11 | |
| α-helix | 293-295 | 3 | |
| α-helix | 301-304 | 4 | |
| α-helix | 309-318 | 10 | |
| α-helix | 323-332 | 10 | |
| α-helix | 343-346 | 4 | |
| α-helix | 353-363 | 11 | |
| 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 | 419-439 | 21 | |
Chain C: 24 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| α-helix | 21-29 | 9 | |
| α-helix | 39-43 | 5 | |
| α-helix | 56-64 | 9 | |
| α-helix | 74-86 | 13 | |
| α-helix | 93-96 | 4 | |
| α-helix | 97-111 | 15 | |
| α-helix | 121-131 | 11 | |
| β-strand | 138 | 1 | 3 |
| α-helix | 140-151 | 12 | |
| α-helix | 159-161 | 3 | |
| α-helix | 165-166 | 2 | |
| β-strand | 169 | 1 | 3 |
| α-helix | 178-194 | 17 | |
| α-helix | 198-209 | 12 | |
| β-strand | 213 | 1 | 2 |
| α-helix | 218-234 | 17 | |
| α-helix | 238-242 | 5 | |
| α-helix | 249-256 | 8 | |
| α-helix | 258-267 | 10 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-310 | 17 | |
| 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 | 370-399 | 30 | |
| α-helix | 402-405 | 4 | |
Chain D: 24 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-14 | 11 | |
| α-helix | 23-31 | 9 | |
| α-helix | 39-53 | 15 | |
| α-helix | 62-72 | 11 | |
| α-helix | 73-75 | 3 | |
| α-helix | 78-92 | 15 | |
| α-helix | 101-115 | 15 | |
| α-helix | 120-128 | 9 | |
| α-helix | 141-157 | 17 | |
| α-helix | 161-175 | 15 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-211 | 11 | |
| α-helix | 219-235 | 17 | |
| α-helix | 237 | 1 | |
| α-helix | 240-251 | 12 | |
| α-helix | 261-268 | 8 | |
| α-helix | 275-278 | 4 | |
| α-helix | 279-283 | 5 | |
| α-helix | 287-290 | 4 | |
| β-strand | 292 | 1 | 4 |
| β-strand | 298 | 1 | 4 |
| α-helix | 300-315 | 16 | |
| β-strand | 316-320 | 5 | 1 |
| α-helix | 321-326 | 6 | |
| α-helix | 334-342 | 9 | |
| β-strand | 351-353 | 3 | 1 |
| β-strand | 358-360 | 3 | 1 |
| α-helix | 367-391 | 25 | |
| α-helix | 393-404 | 12 | |
Chain E: 12 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-42 | 10 | |
| α-helix | 44-46 | 3 | |
| β-strand | 54-58 | 5 | 5 |
| α-helix | 59-71 | 13 | |
| β-strand | 78-86 | 9 | 5 |
| β-strand | 89-95 | 7 | 5 |
| β-strand | 107 | 1 | 6 |
| α-helix | 112-127 | 16 | |
| β-strand | 132-139 | 8 | 5 |
| α-helix | 149-161 | 13 | |
| β-strand | 167-170 | 4 | 5 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-188 | 6 | 5 |
| α-helix | 189-190 | 2 | |
| α-helix | 218-220 | 3 | |
| β-strand | 221-229 | 9 | 5 |
| α-helix | 232-240 | 9 | |
| α-helix | 246-250 | 5 | |
| α-helix | 259-280 | 22 | |
| α-helix | 299-328 | 30 | |
Chain F: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40-43 | 4 | 7 |
| α-helix | 47-62 | 16 | |
| β-strand | 69-76 | 8 | 7 |
| β-strand | 80-88 | 9 | 7 |
| β-strand | 91-94 | 4 | 8 |
| β-strand | 97-100 | 4 | 8 |
| α-helix | 102-112 | 11 | |
| β-strand | 120-127 | 8 | 7 |
| α-helix | 133-142 | 10 | |
| β-strand | 150-154 | 5 | 7 |
| β-strand | 165-171 | 7 | 7 |
| α-helix | 180-181 | 2 | |
| β-strand | 182-186 | 5 | 7 |
| β-strand | 188 | 1 | 7 |
| α-helix | 194-205 | 12 | |
| α-helix | 216-246 | 31 | |
| α-helix | 254-265 | 12 | |
| α-helix | 273-312 | 40 | |
Chain G: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-19 | 8 | |
| α-helix | 25-36 | 12 | |
| α-helix | 46-48 | 3 | |
| α-helix | 50-53 | 4 | |
| α-helix | 54-56 | 3 | |
| α-helix | 61-71 | 11 | |
| α-helix | 77-80 | 4 | |
| α-helix | 86-88 | 3 | |
| α-helix | 90-107 | 18 | |
| 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 | 167-220 | 54 | |
Chain H: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-25 | 14 | |
| α-helix | 34-46 | 13 | |
| α-helix | 50-59 | 10 | |
| α-helix | 62-67 | 6 | |
| α-helix | 69-82 | 14 | |
| α-helix | 86-93 | 8 | |
| α-helix | 100-102 | 3 | |
| α-helix | 103-122 | 20 | |
| β-strand | 125-127 | 3 | 1 |
| β-strand | 128-129 | 2 | 9 |
| α-helix | 130-137 | 8 | |
| α-helix | 142-145 | 4 | |
| α-helix | 146-151 | 6 | |
| β-strand | 161-162 | 2 | 9 |
| α-helix | 197-208 | 12 | |
3 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 5 | E | protein | 334 | Homo sapiens | Q92905 |
| 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 |
| NEDD8 | I | protein | 81 | Homo sapiens | Q15843 |
| Cullin-2 | J | protein | 745 | Homo sapiens | Q13617 |
| E3 ubiquitin-protein ligase RBX1 | K | protein | 108 | Homo sapiens | P62877 |
Sequence of entity 1 (A), FASTA
>9EFQ_1 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>9EFQ_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>9EFQ_3 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 4 (D), FASTA
>9EFQ_4 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E), FASTA
>9EFQ_5 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLAVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGINVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F), FASTA
>9EFQ_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>9EFQ_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 8 (H), FASTA
>9EFQ_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (I), FASTA
>9EFQ_9 NEDD8 (chains I)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGGGGLRQ
Sequence of entity 10 (J), FASTA
>9EFQ_10 Cullin-2 (chains J)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 11 (K), FASTA
>9EFQ_11 E3 ubiquitin-protein ligase RBX1 (chains K)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Primary citation
CSN5i-3 is an orthosteric molecular glue inhibitor of COP9 signalosome. Shi, H., Wang, X., Yu, C. et al. Nature (2026) 652:1375-1383. DOI 10.1038/s41586-026-10129-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
- 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
- 9EG1 3.52 Å, COP9 signalosome deneddylation complex with cullin-5
Browse structure collections
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