9QO0: COP9 signalosome complex subunit 4
Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure. Determined by electron microscopy at 3.26 Å resolution. Released 18 Feb 2026.
- Method
- Electron microscopy
- Resolution
- 3.26 Å
- Organism
- Homo sapiens
- Chains
- 15
- Atoms
- 29,373
- Mol. weight
- 522.16 kDa
- Ligands
- IHP, ZN
- Released
- 18 Feb 2026
Explore 9QO0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9QO0 contains 188 α-helices and 97 β-strands across 15 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: 23 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-47 | 4 | |
| α-helix | 55-66 | 12 | |
| α-helix | 71-82 | 12 | |
| α-helix | 88-105 | 18 | |
| α-helix | 128-154 | 27 | |
| α-helix | 158-174 | 17 | |
| α-helix | 180-186 | 7 | |
| α-helix | 197-212 | 16 | |
| α-helix | 215-225 | 11 | |
| α-helix | 242-259 | 18 | |
| α-helix | 268-271 | 4 | |
| α-helix | 285-288 | 4 | |
| α-helix | 291-300 | 10 | |
| α-helix | 303-305 | 3 | |
| α-helix | 306-311 | 6 | |
| α-helix | 314-320 | 7 | |
| α-helix | 324-333 | 10 | |
| α-helix | 338-354 | 17 | |
| α-helix | 359-361 | 3 | |
| α-helix | 362-378 | 17 | |
| β-strand | 381-385 | 5 | 3 |
| α-helix | 386-392 | 7 | |
| α-helix | 397-409 | 13 | |
| β-strand | 415-418 | 4 | 3 |
| β-strand | 423-426 | 4 | 3 |
| α-helix | 431-461 | 31 | |
| β-strand | 466 | 1 | 7 |
Chain B: 22 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-42 | 7 | |
| α-helix | 52-60 | 9 | |
| α-helix | 66-81 | 16 | |
| α-helix | 85-92 | 8 | |
| α-helix | 93-99 | 7 | |
| α-helix | 105-117 | 13 | |
| α-helix | 128-139 | 12 | |
| α-helix | 145-161 | 17 | |
| α-helix | 166-171 | 6 | |
| α-helix | 176-180 | 5 | |
| β-strand | 181-182 | 2 | 8 |
| β-strand | 185-186 | 2 | 8 |
| α-helix | 194-208 | 15 | |
| α-helix | 211-220 | 10 | |
| α-helix | 231-248 | 18 | |
| α-helix | 253-268 | 16 | |
| α-helix | 273-286 | 14 | |
| α-helix | 293-295 | 3 | |
| α-helix | 309-320 | 12 | |
| α-helix | 323-332 | 10 | |
| α-helix | 347-363 | 17 | |
| β-strand | 366-370 | 5 | 3 |
| α-helix | 371-378 | 8 | |
| α-helix | 382-394 | 13 | |
| β-strand | 400-403 | 4 | 3 |
| β-strand | 408-411 | 4 | 3 |
| α-helix | 419-439 | 21 | |
Chain C: 20 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-64 | 12 | |
| α-helix | 74-87 | 14 | |
| α-helix | 91-95 | 5 | |
| α-helix | 99-113 | 15 | |
| α-helix | 121-131 | 11 | |
| β-strand | 138 | 1 | 9 |
| α-helix | 140-152 | 13 | |
| α-helix | 159-162 | 4 | |
| β-strand | 169 | 1 | 9 |
| α-helix | 178-194 | 17 | |
| α-helix | 198-209 | 12 | |
| β-strand | 213 | 1 | 7 |
| α-helix | 218-234 | 17 | |
| α-helix | 238-242 | 5 | |
| α-helix | 253-256 | 4 | |
| α-helix | 258-268 | 11 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-311 | 18 | |
| β-strand | 314-318 | 5 | 3 |
| α-helix | 319-326 | 8 | |
| α-helix | 331-344 | 14 | |
| β-strand | 349-352 | 4 | 3 |
| β-strand | 357-360 | 4 | 3 |
| α-helix | 372-398 | 27 | |
| α-helix | 401-407 | 7 | |
Chain D: 24 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-14 | 10 | |
| α-helix | 22-35 | 14 | |
| α-helix | 41-52 | 12 | |
| α-helix | 63-71 | 9 | |
| α-helix | 78-91 | 14 | |
| α-helix | 93-95 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 110-116 | 7 | |
| α-helix | 141-156 | 16 | |
| α-helix | 161-174 | 14 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-211 | 11 | |
| α-helix | 219-234 | 16 | |
| α-helix | 241-251 | 11 | |
| α-helix | 254-256 | 3 | |
| α-helix | 261-268 | 8 | |
| α-helix | 275-278 | 4 | |
| α-helix | 279-284 | 6 | |
| α-helix | 287-290 | 4 | |
| β-strand | 292 | 1 | 1 |
| β-strand | 298 | 1 | 1 |
| α-helix | 299-312 | 14 | |
| β-strand | 316 | 1 | 2 |
| β-strand | 318-320 | 3 | 3 |
| α-helix | 321-327 | 7 | |
| α-helix | 332-345 | 14 | |
| β-strand | 351-353 | 3 | 3 |
| β-strand | 358-360 | 3 | 3 |
| α-helix | 366-391 | 26 | |
| α-helix | 393-402 | 10 | |
Chain E: 13 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-42 | 10 | |
| β-strand | 54-58 | 5 | 10 |
| α-helix | 59-71 | 13 | |
| β-strand | 78-81 | 4 | 11 |
| β-strand | 89-92 | 4 | 10 |
| β-strand | 95-97 | 3 | 11 |
| α-helix | 98-100 | 3 | |
| α-helix | 111-126 | 16 | |
| β-strand | 135-139 | 5 | 11 |
| α-helix | 149-160 | 12 | |
| β-strand | 166-170 | 5 | 11 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-188 | 6 | 11 |
| α-helix | 189-190 | 2 | |
| α-helix | 211-216 | 6 | |
| β-strand | 221-223 | 3 | 11 |
| β-strand | 225-229 | 5 | 10 |
| α-helix | 232-241 | 10 | |
| α-helix | 242-245 | 4 | |
| α-helix | 246-249 | 4 | |
| α-helix | 259-279 | 21 | |
| α-helix | 299-328 | 30 | |
Chain F: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 41-43 | 3 | 12 |
| α-helix | 45-61 | 17 | |
| β-strand | 70-75 | 6 | 12 |
| β-strand | 81-88 | 8 | 12 |
| β-strand | 91-93 | 3 | 13 |
| β-strand | 98-100 | 3 | 13 |
| α-helix | 103-113 | 11 | |
| β-strand | 120-127 | 8 | 12 |
| α-helix | 135-143 | 9 | |
| β-strand | 150-154 | 5 | 12 |
| β-strand | 165-167 | 3 | 12 |
| β-strand | 168-170 | 3 | 14 |
| β-strand | 183-185 | 3 | 14 |
| β-strand | 188-190 | 3 | 12 |
| α-helix | 194-206 | 13 | |
| α-helix | 216-247 | 32 | |
| α-helix | 255-265 | 11 | |
| α-helix | 273-312 | 40 | |
Chain G: 13 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-16 | 5 | |
| α-helix | 24-34 | 11 | |
| α-helix | 45-48 | 4 | |
| α-helix | 50-53 | 4 | |
| α-helix | 54-56 | 3 | |
| α-helix | 61-72 | 12 | |
| α-helix | 75-80 | 6 | |
| α-helix | 86-89 | 4 | |
| α-helix | 90-107 | 18 | |
| β-strand | 110-112 | 3 | 2 |
| α-helix | 113-120 | 8 | |
| α-helix | 125-137 | 13 | |
| β-strand | 143-146 | 4 | 2 |
| β-strand | 151-154 | 4 | 2 |
| α-helix | 158-161 | 4 | |
| α-helix | 164-222 | 59 | |
Chain H: 12 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-26 | 14 | |
| α-helix | 28-30 | 3 | |
| α-helix | 34-47 | 14 | |
| α-helix | 50-59 | 10 | |
| α-helix | 62-67 | 6 | |
| α-helix | 70-83 | 14 | |
| α-helix | 86-93 | 8 | |
| α-helix | 103-124 | 22 | |
| β-strand | 125-127 | 3 | 3 |
| β-strand | 128-129 | 2 | 15 |
| α-helix | 130-136 | 7 | |
| α-helix | 141-146 | 6 | |
| α-helix | 149-151 | 3 | |
| β-strand | 154-156 | 3 | 15 |
| β-strand | 161-163 | 3 | 15 |
| α-helix | 197-208 | 12 | |
7 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 4 | D | protein | 406 | Homo sapiens | Q9BT78 (AlphaFold model) |
| COP9 signalosome complex subunit 7b | G | protein | 264 | Homo sapiens | Q9H9Q2 (AlphaFold model) |
| NEDD8 | K | protein | 76 | Homo sapiens | Q15843 (AlphaFold model) |
| Cyclin-dependent kinases regulatory subunit 1 | N | protein | 79 | Homo sapiens | P61024 (AlphaFold model) |
| COP9 signalosome complex subunit 9 | P | protein | 57 | Homo sapiens | Q8WXC6 |
| COP9 signalosome complex subunit 1 | A | protein | 491 | Homo sapiens | Q13098 |
| COP9 signalosome complex subunit 2 | B | protein | 443 | Homo sapiens | P61201 |
| COP9 signalosome complex subunit 3 | C | protein | 423 | Homo sapiens | Q9UNS2 |
| 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 8 | H | protein | 209 | Homo sapiens | Q99627 |
| Cullin-1 | I | protein | 776 | Homo sapiens | Q13616 |
3 more molecules are not listed.
Sequence of entity 1 (D), FASTA
>9QO0_1 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 2 (G), FASTA
>9QO0_2 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 3 (K), FASTA
>9QO0_3 NEDD8 (chains K)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG
Sequence of entity 4 (N), FASTA
>9QO0_4 Cyclin-dependent kinases regulatory subunit 1 (chains N)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK
Sequence of entity 5 (P), FASTA
>9QO0_5 COP9 signalosome complex subunit 9 (chains P)
MKPAVDEMFPEGAGPYVDLDEAGGSTGLLMDLAANEKAVHADFFNDFEDLFDDDDIQ
Sequence of entity 6 (A), FASTA
>9QO0_6 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 7 (B), FASTA
>9QO0_7 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 8 (C), FASTA
>9QO0_8 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 9 (E), FASTA
>9QO0_9 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 10 (F), FASTA
>9QO0_10 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 11 (H), FASTA
>9QO0_11 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 12 (I), FASTA
>9QO0_12 Cullin-1 (chains I)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| IHP | Inositol hexakisphosphate | C6 H18 O24 P6 | 1 |
| ZN | Zinc ion | Zn | 3 |
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 Q9BT78 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4D0P 1.6 Å, Crystal structure of human CSN4
- 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
- 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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