4D18: COP9 signalosome
Crystal structure of the COP9 signalosome. Determined by X-ray diffraction at 4.08 Å resolution. Released 23 Jul 2014.
- Method
- X-ray diffraction
- Resolution
- 4.08 Å
- Organism
- HOMO SAPIENS
- Chains
- 16
- Atoms
- 41,422
- Mol. weight
- 645.74 kDa
- Ligands
- ZN
- Released
- 23 Jul 2014
Explore 4D18 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4D18 contains 286 α-helices and 88 β-strands across 16 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.
Chains A and I: 25 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 84-90 | 7 | |
| α-helix | 94-106 | 13 | |
| α-helix | 111-122 | 12 | |
| α-helix | 129-147 | 19 | |
| α-helix | 164-191 | 28 | |
| α-helix | 194-211 | 18 | |
| α-helix | 216-224 | 9 | |
| α-helix | 225-227 | 3 | |
| α-helix | 231-248 | 18 | |
| α-helix | 251-263 | 13 | |
| α-helix | 282-295 | 14 | |
| α-helix | 299-306 | 8 | |
| α-helix | 311-313 | 3 | |
| α-helix | 322-336 | 15 | |
| α-helix | 339-342 | 4 | |
| α-helix | 343-347 | 5 | |
| α-helix | 350-358 | 9 | |
| α-helix | 360-370 | 11 | |
| α-helix | 374-388 | 15 | |
| α-helix | 395-397 | 3 | |
| α-helix | 398-414 | 17 | |
| β-strand | 417-421 | 5 | 1 |
| α-helix | 422-428 | 7 | |
| α-helix | 433-445 | 13 | |
| β-strand | 451-454 | 4 | 1 |
| β-strand | 459-462 | 4 | 1 |
| α-helix | 463 | 1 | |
| α-helix | 467-498 | 32 | |
| β-strand | 502 | 1 | 2 |
Chains B and J: 22 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-41 | 10 | |
| α-helix | 50-59 | 10 | |
| α-helix | 66-79 | 14 | |
| α-helix | 86-95 | 10 | |
| α-helix | 105-122 | 18 | |
| α-helix | 125-138 | 14 | |
| α-helix | 146-162 | 17 | |
| α-helix | 166-177 | 12 | |
| α-helix | 194-208 | 15 | |
| α-helix | 211-224 | 14 | |
| α-helix | 233-248 | 16 | |
| α-helix | 251-268 | 18 | |
| α-helix | 272-286 | 15 | |
| α-helix | 301-304 | 4 | |
| α-helix | 309-320 | 12 | |
| α-helix | 323-332 | 10 | |
| α-helix | 334-338 | 5 | |
| α-helix | 341-344 | 4 | |
| α-helix | 347-363 | 17 | |
| 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 | 418-439 | 22 | |
Chains C and K: 25 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-15 | 11 | |
| α-helix | 22-30 | 9 | |
| α-helix | 39-42 | 4 | |
| α-helix | 54-64 | 11 | |
| α-helix | 74-83 | 10 | |
| α-helix | 84-88 | 5 | |
| α-helix | 97-113 | 17 | |
| α-helix | 119-131 | 13 | |
| β-strand | 138 | 1 | 3 |
| α-helix | 141-151 | 11 | |
| α-helix | 156-161 | 6 | |
| β-strand | 169 | 1 | 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 | 247-248 | 2 | |
| α-helix | 249-253 | 5 | |
| α-helix | 254-256 | 3 | |
| α-helix | 258-267 | 10 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-308 | 15 | |
| 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 | 401-402 | 2 | |
Chain D: 26 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-12 | 11 | |
| α-helix | 19-34 | 16 | |
| α-helix | 39-52 | 14 | |
| α-helix | 59-72 | 14 | |
| α-helix | 73-75 | 3 | |
| α-helix | 78-92 | 15 | |
| α-helix | 93-99 | 7 | |
| α-helix | 100-116 | 17 | |
| α-helix | 120-128 | 9 | |
| α-helix | 141-157 | 17 | |
| α-helix | 161-175 | 15 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-212 | 12 | |
| α-helix | 219-235 | 17 | |
| α-helix | 237 | 1 | |
| α-helix | 240-251 | 12 | |
| β-strand | 252 | 1 | 4 |
| α-helix | 253-257 | 5 | |
| α-helix | 261-268 | 8 | |
| α-helix | 271-274 | 4 | |
| α-helix | 275-283 | 9 | |
| α-helix | 287-290 | 4 | |
| β-strand | 292-293 | 2 | 5 |
| β-strand | 297-298 | 2 | 5 |
| α-helix | 299-313 | 15 | |
| 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 | 367-391 | 25 | |
| α-helix | 393-405 | 13 | |
Chains E and M: 15 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 33-42 | 10 | |
| α-helix | 44-47 | 4 | |
| β-strand | 54-58 | 5 | 6 |
| α-helix | 59-71 | 13 | |
| β-strand | 78-86 | 9 | 6 |
| β-strand | 89-97 | 9 | 6 |
| α-helix | 109-113 | 5 | |
| α-helix | 114-126 | 13 | |
| β-strand | 132-139 | 8 | 6 |
| α-helix | 149-161 | 13 | |
| β-strand | 166-170 | 5 | 6 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-188 | 6 | 6 |
| α-helix | 189-190 | 2 | |
| α-helix | 193-195 | 3 | |
| α-helix | 208-217 | 10 | |
| β-strand | 221-223 | 3 | 6 |
| β-strand | 225-229 | 5 | 6 |
| α-helix | 232-249 | 18 | |
| α-helix | 254-257 | 4 | |
| α-helix | 259-281 | 23 | |
| α-helix | 299-328 | 30 | |
Chain F: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40-43 | 4 | 4 |
| α-helix | 45-62 | 18 | |
| β-strand | 69-77 | 9 | 4 |
| β-strand | 80-88 | 9 | 4 |
| β-strand | 91-94 | 4 | 7 |
| β-strand | 97-100 | 4 | 7 |
| α-helix | 102-115 | 14 | |
| β-strand | 120-127 | 8 | 4 |
| α-helix | 133-143 | 11 | |
| β-strand | 150-154 | 5 | 4 |
| β-strand | 165-175 | 11 | 4 |
| β-strand | 178-186 | 9 | 4 |
| β-strand | 188-190 | 3 | 4 |
| α-helix | 194-205 | 12 | |
| α-helix | 222-247 | 26 | |
| α-helix | 251-252 | 2 | |
| α-helix | 254-264 | 11 | |
| α-helix | 267 | 1 | |
| α-helix | 273-312 | 40 | |
Chains G and O: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-19 | 10 | |
| α-helix | 24-34 | 11 | |
| α-helix | 44-47 | 4 | |
| α-helix | 50-53 | 4 | |
| α-helix | 61-71 | 11 | |
| α-helix | 75-80 | 6 | |
| α-helix | 86-87 | 2 | |
| 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 | 168-212 | 45 | |
Chains H and P: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-26 | 15 | |
| α-helix | 34-46 | 13 | |
| α-helix | 50-57 | 8 | |
| α-helix | 62-67 | 6 | |
| α-helix | 69-83 | 15 | |
| α-helix | 86-93 | 8 | |
| α-helix | 103-124 | 22 | |
| β-strand | 125-127 | 3 | 1 |
| β-strand | 128-129 | 2 | 8 |
| α-helix | 130-137 | 8 | |
| α-helix | 141-151 | 11 | |
| β-strand | 154-156 | 3 | 8 |
| β-strand | 161-163 | 3 | 8 |
| α-helix | 197-208 | 12 | |
2 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, I | protein | 480 | HOMO SAPIENS | Q13098 (AlphaFold model) |
| COP9 signalosome complex subunit 2 | B, J | protein | 447 | HOMO SAPIENS | P61201 (AlphaFold model) |
| COP9 signalosome complex subunit 3 | C, K | protein | 427 | HOMO SAPIENS | Q9UNS2 (AlphaFold model) |
| COP9 signalosome complex subunit 4 | D, L | protein | 410 | HOMO SAPIENS | Q9BT78 (AlphaFold model) |
| COP9 signalosome complex subunit 5 | E, M | protein | 327 | HOMO SAPIENS | Q92905 |
| COP9 signalosome complex subunit 6 | F, N | protein | 331 | HOMO SAPIENS | Q7L5N1 |
| COP9 signalosome complex subunit 7A | G, O | protein | 222 | HOMO SAPIENS | Q9UBW8 |
| COP9 signalosome complex subunit 8 | H, P | protein | 213 | HOMO SAPIENS | Q99627 |
Sequence of entity 1 (A, I), FASTA
>4D18_1 COP9 SIGNALOSOME COMPLEX SUBUNIT 1 (chains A, I)
GGGRGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERLQFIADHC
PTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRELQNAPDAIPESGVEPPALDTAWV
EATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDY
CTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKC
AAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALATFDRQELQRNVI
SSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAPHVRTLYTQIRN
RALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSHSKILYARDVDQ
RSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM
Sequence of entity 2 (B, J), FASTA
>4D18_2 COP9 SIGNALOSOME COMPLEX SUBUNIT 2 (chains B, J)
GGGRMSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQK
VLELEGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSIL
DYISTSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLH
QSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGV
IRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDS
QEAKPYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRT
QVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKR
GGARYTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C, K), FASTA
>4D18_3 COP9 SIGNALOSOME COMPLEX SUBUNIT 3 (chains C, K)
GGGRMASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSL
GVLAVLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQ
PLRGIGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAY
DAKHFLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLG
KVQQLPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVK
QCLSSLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDG
MVSFHDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSG
NKPSSYS
Sequence of entity 4 (D, L), FASTA
>4D18_4 COP9 SIGNALOSOME COMPLEX SUBUNIT 4 (chains D, L)
GGGRMAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNEN
VSLVISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEK
EEDWRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQN
ESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILA
SAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADG
SSILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQID
GIVHFETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E, M), FASTA
>4D18_5 COP9 SIGNALOSOME COMPLEX SUBUNIT 5 (chains E, M)
GGGRTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVM
HARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQV
GRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFR
TYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWV
NTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKLAKATRDS
CKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F, N), FASTA
>4D18_6 COP9 SIGNALOSOME COMPLEX SUBUNIT 6 (chains F, N)
GGGRMAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWI
RMRSQEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVF
KELEFLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIIN
GEATMLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVK
LILEYVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTIT
KTCNTMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G, O), FASTA
>4D18_7 COP9 SIGNALOSOME COMPLEX SUBUNIT 7A (chains G, O)
GGGRMSAEVKVTGQNQEQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELA
ESDFASTFRLLTVFAYGTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVL
LEALALRNVRQLEDLVIEAVYADVLRGSLDQRNQRLEVDYSIGRDIQRQDLSAIARTLQE
WCVGCEVVLSGIEEQVSRANQHKEQQLGLKQQIESEVANLKK
Sequence of entity 8 (H, P), FASTA
>4D18_8 COP9 SIGNALOSOME COMPLEX SUBUNIT 8 (chains H, P)
GGGRMPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYL
WKRIPPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRR
AFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSF
NKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Crystal Structure of the Human Cop9 Signalosome. Lingaraju, G.M., Bunker, R.D., Cavadini, S. et al. Nature (2014) 512:161. DOI 10.1038/NATURE13566 · 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
About this viewer
MolViewer shows 4D18 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.