6R7I: COP9 signalosome complex subunit 1
Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome. Determined by electron microscopy at 5.9 Å resolution. Released 28 Aug 2019.
- Method
- Electron microscopy
- Resolution
- 5.9 Å
- Organism
- Homo sapiens
- Chains
- 13
- Atoms
- 30,122
- Mol. weight
- 446.83 kDa
- Ligands
- ZN
- Released
- 28 Aug 2019
Explore 6R7I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6R7I contains 184 α-helices and 67 β-strands across 13 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: 25 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 84-90 | 7 | |
| α-helix | 93-105 | 13 | |
| α-helix | 111-122 | 12 | |
| α-helix | 128-145 | 22 | |
| α-helix | 164-191 | 28 | |
| α-helix | 194-210 | 17 | |
| α-helix | 215-224 | 10 | |
| α-helix | 225-227 | 3 | |
| α-helix | 231-248 | 18 | |
| α-helix | 251-263 | 13 | |
| α-helix | 272-277 | 6 | |
| α-helix | 282-295 | 14 | |
| α-helix | 299-306 | 8 | |
| α-helix | 311-313 | 3 | |
| α-helix | 322-336 | 15 | |
| α-helix | 339-346 | 8 | |
| α-helix | 353-356 | 4 | |
| α-helix | 360-370 | 11 | |
| α-helix | 374-381 | 8 | |
| α-helix | 385-390 | 6 | |
| α-helix | 395-397 | 3 | |
| α-helix | 398-414 | 17 | |
| β-strand | 417-419 | 3 | 1 |
| β-strand | 421 | 1 | 2 |
| α-helix | 423-429 | 7 | |
| α-helix | 433-446 | 14 | |
| β-strand | 452-454 | 3 | 2 |
| β-strand | 459-461 | 3 | 2 |
| α-helix | 468-497 | 30 | |
Chain B: 21 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-16 | 11 | |
| α-helix | 31-41 | 11 | |
| α-helix | 51-59 | 9 | |
| α-helix | 67-81 | 15 | |
| α-helix | 85-96 | 12 | |
| α-helix | 105-121 | 17 | |
| α-helix | 125-138 | 14 | |
| α-helix | 147-158 | 12 | |
| α-helix | 166-179 | 14 | |
| α-helix | 194-208 | 15 | |
| α-helix | 211-221 | 11 | |
| α-helix | 234-248 | 15 | |
| α-helix | 252-268 | 17 | |
| α-helix | 273-287 | 15 | |
| α-helix | 299-302 | 4 | |
| α-helix | 306-319 | 14 | |
| α-helix | 323-332 | 10 | |
| α-helix | 341-363 | 23 | |
| β-strand | 368-369 | 2 | 3 |
| α-helix | 371-378 | 8 | |
| α-helix | 382-394 | 13 | |
| β-strand | 402-403 | 2 | 1 |
| β-strand | 409-410 | 2 | 3 |
| α-helix | 418-439 | 22 | |
Chain C: 24 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 11-15 | 5 | |
| α-helix | 25-27 | 3 | |
| α-helix | 40-43 | 4 | |
| α-helix | 57-62 | 6 | |
| α-helix | 76-86 | 11 | |
| α-helix | 93-96 | 4 | |
| α-helix | 97-99 | 3 | |
| α-helix | 100-105 | 6 | |
| α-helix | 106-114 | 9 | |
| α-helix | 121-131 | 11 | |
| α-helix | 140-151 | 12 | |
| α-helix | 178-194 | 17 | |
| α-helix | 198-209 | 12 | |
| α-helix | 218-229 | 12 | |
| α-helix | 230-234 | 5 | |
| α-helix | 249-256 | 8 | |
| α-helix | 258-267 | 10 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-286 | 4 | |
| α-helix | 294-313 | 20 | |
| β-strand | 316 | 1 | 2 |
| α-helix | 319-325 | 7 | |
| α-helix | 331-343 | 13 | |
| β-strand | 351-352 | 2 | 4 |
| β-strand | 357 | 1 | 4 |
| α-helix | 370-397 | 28 | |
Chain D: 26 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-12 | 12 | |
| α-helix | 19-34 | 16 | |
| α-helix | 39-52 | 14 | |
| α-helix | 59-71 | 13 | |
| α-helix | 73-75 | 3 | |
| α-helix | 79-92 | 14 | |
| α-helix | 96-98 | 3 | |
| α-helix | 100-116 | 17 | |
| α-helix | 120-128 | 9 | |
| α-helix | 141-158 | 18 | |
| α-helix | 161-170 | 10 | |
| α-helix | 173-176 | 4 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-212 | 12 | |
| α-helix | 219-235 | 17 | |
| α-helix | 240-251 | 12 | |
| α-helix | 254-257 | 4 | |
| α-helix | 259-266 | 8 | |
| α-helix | 267-269 | 3 | |
| α-helix | 281-284 | 4 | |
| α-helix | 287-290 | 4 | |
| α-helix | 299-315 | 17 | |
| β-strand | 318-320 | 3 | 5 |
| α-helix | 321-327 | 7 | |
| α-helix | 332-345 | 14 | |
| β-strand | 352-353 | 2 | 5 |
| β-strand | 358-360 | 3 | 5 |
| α-helix | 367-391 | 25 | |
| α-helix | 393-405 | 13 | |
Chain E: 13 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| α-helix | 33-40 | 8 | |
| α-helix | 44-47 | 4 | |
| β-strand | 54-57 | 4 | 6 |
| α-helix | 60-70 | 11 | |
| β-strand | 77 | 1 | 7 |
| α-helix | 80 | 1 | |
| β-strand | 81-86 | 6 | 6 |
| β-strand | 89-92 | 4 | 6 |
| α-helix | 110-113 | 4 | |
| α-helix | 115-124 | 10 | |
| α-helix | 125-127 | 3 | |
| β-strand | 132-135 | 4 | 6 |
| β-strand | 139 | 1 | 7 |
| β-strand | 140 | 1 | 8 |
| β-strand | 144 | 1 | 8 |
| α-helix | 149-162 | 14 | |
| β-strand | 168-169 | 2 | 9 |
| β-strand | 184-188 | 5 | 9 |
| α-helix | 208-217 | 10 | |
| β-strand | 221-224 | 4 | 9 |
| β-strand | 225 | 1 | 6 |
| β-strand | 228 | 1 | 6 |
| α-helix | 232-249 | 18 | |
| α-helix | 259-280 | 22 | |
| α-helix | 299-329 | 31 | |
Chain F: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40 | 1 | 10 |
| α-helix | 46-62 | 17 | |
| β-strand | 70-72 | 3 | 11 |
| β-strand | 73-77 | 5 | 10 |
| β-strand | 80-85 | 6 | 10 |
| β-strand | 88 | 1 | 11 |
| β-strand | 91-94 | 4 | 12 |
| β-strand | 97-100 | 4 | 12 |
| α-helix | 102-112 | 11 | |
| β-strand | 123-125 | 3 | 11 |
| β-strand | 127 | 1 | 13 |
| α-helix | 133-142 | 10 | |
| β-strand | 150-153 | 4 | 11 |
| β-strand | 154 | 1 | 13 |
| β-strand | 166-175 | 10 | 11 |
| β-strand | 178-185 | 8 | 11 |
| α-helix | 194-205 | 12 | |
| α-helix | 216-247 | 32 | |
| α-helix | 258-264 | 7 | |
| α-helix | 273-311 | 39 | |
Chain G: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-21 | 11 | |
| α-helix | 25-34 | 10 | |
| α-helix | 50-55 | 6 | |
| α-helix | 61-71 | 11 | |
| α-helix | 75-80 | 6 | |
| α-helix | 90-107 | 18 | |
| α-helix | 113-119 | 7 | |
| α-helix | 125-137 | 13 | |
| β-strand | 141 | 1 | 14 |
| β-strand | 145-146 | 2 | 15 |
| β-strand | 151-152 | 2 | 15 |
| β-strand | 157 | 1 | 14 |
| α-helix | 167-214 | 48 | |
Chain H: 10 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-26 | 15 | |
| α-helix | 34-45 | 12 | |
| α-helix | 51-57 | 7 | |
| 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 | 4 |
| β-strand | 129 | 1 | 16 |
| α-helix | 130-135 | 6 | |
| α-helix | 141-150 | 10 | |
| β-strand | 161 | 1 | 16 |
| α-helix | 197-207 | 11 | |
5 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 | 462 | 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 | 401 | Homo sapiens | Q9UNS2 (AlphaFold model) |
| COP9 signalosome complex subunit 4 | D | protein | 407 | 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 | 215 | Homo sapiens | Q9H9Q2 |
| COP9 signalosome complex subunit 8 | H | protein | 209 | Homo sapiens | Q99627 |
| NEDD8 | N | protein | 78 | Homo sapiens | Q15843 |
| Cullin-2 | O | protein | 745 | Homo sapiens | Q13617 |
| Elongin-B | P | protein | 106 | Homo sapiens | Q15370 |
| Elongin-C | Q | protein | 99 | Homo sapiens | Q03071 |
1 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6R7I_1 COP9 signalosome complex subunit 1 (chains A)
KVYIEKDVENPSLDLEQYAASYSGLMRIERLQFIADHCPTLRVEALKMALSFVQRTFNVD
MYEEIHRKLSEATRSSLRELQNAPDAIPESGVEPPALDTAWVEATRKKALLKLEKLDTDL
KNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDYCTSAKHVINMCLNVIKVS
VYLQNWSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKCAAGLAELAARKYKQAAKC
LLLASFDHCDFPELLSPSNVAIYGGLCALATFDRQELQRNVISSSSFKLFLELEPQVRDI
IFKFYESKYASCLKMLDEMKDNLLLDMYLAPHVRTLYTQIRNRALIQYFSPYVSADMHRM
AAAFNTTVAALEDELTQLILEGLISARVDSHSKILYARDVDQRSTTFEKSLLMGKEFQRR
AKAMMLRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>6R7I_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>6R7I_3 COP9 signalosome complex subunit 3 (chains C)
SALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLAVL
FVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRGIG
ILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKHFL
CYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQLP
KYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLSSL
YKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSFHD
NPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQF
Sequence of entity 4 (D), FASTA
>6R7I_4 COP9 signalosome complex subunit 4 (chains D)
RMAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSL
VISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEED
WRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNEST
NEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAG
QQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSI
LDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIV
HFETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E), FASTA
>6R7I_5 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F), FASTA
>6R7I_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>6R7I_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDLSAIARTLQEWCVG
CEVVLSGIEEQVSRANQHKEQQLGLKQQIESEVAN
Sequence of entity 8 (H), FASTA
>6R7I_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (N), FASTA
>6R7I_9 NEDD8 (chains N)
GSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAAD
YKIMGGSVLHLVLALRGG
Sequence of entity 10 (O), FASTA
>6R7I_10 Cullin-2 (chains O)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 11 (P), FASTA
>6R7I_11 Elongin-B (chains P)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQ
Sequence of entity 12 (Q), FASTA
>6R7I_12 Elongin-C (chains Q)
MSQDFVTLVSKDDKEYEISRSAAMISPTLKAMIEGPFRESKGRIELKQFDSHILEKAVEY
LNYNLKYSGVSEDDDEIPEFEIPTEMSLELLLAADYLSI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome. Faull, S.V., Lau, A.M.C., Martens, C. et al. Nat Commun (2019) 10:3814-3814. DOI 10.1038/s41467-019-11772-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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