6R6H: COP9 signalosome complex subunit 1
Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome. Determined by electron microscopy at 8.4 Å resolution. Released 28 Aug 2019.
- Method
- Electron microscopy
- Resolution
- 8.4 Å
- Organism
- Homo sapiens
- Chains
- 13
- Atoms
- 30,606
- Mol. weight
- 455.96 kDa
- Ligands
- ZN
- Released
- 28 Aug 2019
Explore 6R6H in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6R6H contains 185 α-helices and 74 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: 22 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 84-90 | 7 | |
| α-helix | 93-105 | 13 | |
| α-helix | 111-122 | 12 | |
| α-helix | 129-145 | 21 | |
| α-helix | 165-191 | 27 | |
| α-helix | 194-209 | 16 | |
| α-helix | 214-224 | 11 | |
| α-helix | 231-248 | 18 | |
| α-helix | 252-263 | 12 | |
| α-helix | 272-276 | 5 | |
| α-helix | 281-296 | 16 | |
| α-helix | 299-308 | 10 | |
| α-helix | 322-336 | 15 | |
| α-helix | 339-341 | 3 | |
| α-helix | 342-346 | 5 | |
| α-helix | 353-358 | 6 | |
| α-helix | 360-371 | 12 | |
| α-helix | 374-390 | 17 | |
| α-helix | 398-414 | 17 | |
| β-strand | 417-419 | 3 | 1 |
| α-helix | 422-429 | 8 | |
| α-helix | 433-445 | 13 | |
| β-strand | 452 | 1 | 2 |
| β-strand | 461 | 1 | 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: 25 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-13 | 6 | |
| α-helix | 22-26 | 5 | |
| α-helix | 38-44 | 7 | |
| α-helix | 55-65 | 11 | |
| α-helix | 72-74 | 3 | |
| α-helix | 76-86 | 11 | |
| α-helix | 97-113 | 17 | |
| α-helix | 120-129 | 10 | |
| α-helix | 141-151 | 11 | |
| α-helix | 156-158 | 3 | |
| α-helix | 159-163 | 5 | |
| α-helix | 178-194 | 17 | |
| α-helix | 198-210 | 13 | |
| α-helix | 218-229 | 12 | |
| α-helix | 230-234 | 5 | |
| α-helix | 238-241 | 4 | |
| α-helix | 247-248 | 2 | |
| α-helix | 249-253 | 5 | |
| α-helix | 258-269 | 12 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-313 | 20 | |
| α-helix | 321-325 | 5 | |
| α-helix | 330-343 | 14 | |
| β-strand | 352 | 1 | 4 |
| β-strand | 357 | 1 | 4 |
| α-helix | 370-399 | 30 | |
Chain D: 25 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 19-27 | 9 | |
| α-helix | 31-34 | 4 | |
| α-helix | 39-52 | 14 | |
| α-helix | 59-75 | 17 | |
| α-helix | 78-91 | 14 | |
| α-helix | 97-99 | 3 | |
| α-helix | 100-117 | 18 | |
| α-helix | 120-128 | 9 | |
| α-helix | 141-158 | 18 | |
| α-helix | 161-171 | 11 | |
| α-helix | 172-174 | 3 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-213 | 13 | |
| α-helix | 219-235 | 17 | |
| α-helix | 240-251 | 12 | |
| α-helix | 254-257 | 4 | |
| α-helix | 261-268 | 8 | |
| α-helix | 275-283 | 9 | |
| α-helix | 300-310 | 11 | |
| β-strand | 318-320 | 3 | 5 |
| α-helix | 321-327 | 7 | |
| α-helix | 333-344 | 12 | |
| α-helix | 354-356 | 3 | |
| β-strand | 358-360 | 3 | 5 |
| α-helix | 367-385 | 19 | |
| β-strand | 388 | 1 | 6 |
| β-strand | 392 | 1 | 6 |
| α-helix | 393-403 | 11 | |
Chain E: 15 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 | 7 |
| α-helix | 60-70 | 11 | |
| β-strand | 77 | 1 | 8 |
| α-helix | 80 | 1 | |
| β-strand | 81-86 | 6 | 7 |
| β-strand | 89-92 | 4 | 7 |
| α-helix | 110-113 | 4 | |
| α-helix | 115-124 | 10 | |
| α-helix | 125-127 | 3 | |
| β-strand | 132-135 | 4 | 7 |
| β-strand | 139 | 1 | 8 |
| β-strand | 140 | 1 | 9 |
| β-strand | 144 | 1 | 9 |
| α-helix | 149-162 | 14 | |
| β-strand | 168-169 | 2 | 10 |
| β-strand | 184-188 | 5 | 10 |
| α-helix | 208-217 | 10 | |
| β-strand | 221-224 | 4 | 10 |
| β-strand | 225 | 1 | 7 |
| β-strand | 228 | 1 | 7 |
| α-helix | 232-249 | 18 | |
| α-helix | 256-258 | 3 | |
| α-helix | 261-278 | 18 | |
| α-helix | 300-324 | 25 | |
| α-helix | 325-329 | 5 | |
Chain F: 9 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40 | 1 | 12 |
| α-helix | 46-62 | 17 | |
| β-strand | 70-72 | 3 | 13 |
| β-strand | 73-77 | 5 | 12 |
| β-strand | 80-85 | 6 | 12 |
| β-strand | 88 | 1 | 13 |
| β-strand | 91-94 | 4 | 14 |
| β-strand | 97-100 | 4 | 14 |
| α-helix | 102-112 | 11 | |
| β-strand | 123-125 | 3 | 13 |
| β-strand | 127 | 1 | 15 |
| α-helix | 133-142 | 10 | |
| β-strand | 150-153 | 4 | 13 |
| β-strand | 154 | 1 | 15 |
| β-strand | 166-175 | 10 | 13 |
| β-strand | 178-185 | 8 | 13 |
| α-helix | 194-205 | 12 | |
| α-helix | 222-245 | 24 | |
| α-helix | 254 | 1 | |
| α-helix | 255-260 | 6 | |
| α-helix | 261-266 | 6 | |
| α-helix | 275-312 | 38 | |
Chain G: 11 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-21 | 12 | |
| α-helix | 24-35 | 12 | |
| α-helix | 46-48 | 3 | |
| α-helix | 50-55 | 6 | |
| α-helix | 61-71 | 11 | |
| α-helix | 75-80 | 6 | |
| α-helix | 86-87 | 2 | |
| α-helix | 90-107 | 18 | |
| α-helix | 113-119 | 7 | |
| α-helix | 125-137 | 13 | |
| β-strand | 145-146 | 2 | 30 |
| β-strand | 151-152 | 2 | 30 |
| α-helix | 167-213 | 47 | |
Chain H: 11 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-26 | 15 | |
| α-helix | 34-46 | 13 | |
| α-helix | 52-57 | 6 | |
| α-helix | 62-67 | 6 | |
| α-helix | 69-83 | 15 | |
| α-helix | 86-93 | 8 | |
| α-helix | 103-119 | 17 | |
| α-helix | 120-124 | 5 | |
| β-strand | 127 | 1 | 4 |
| β-strand | 128 | 1 | 16 |
| α-helix | 130-136 | 7 | |
| α-helix | 141-150 | 10 | |
| β-strand | 154 | 1 | 17 |
| β-strand | 162 | 1 | 16 |
| β-strand | 163 | 1 | 17 |
| α-helix | 195-207 | 13 | |
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 | 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 | 403 | 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 | 308 | Homo sapiens | Q7L5N1 |
| COP9 signalosome complex subunit 8 | H | protein | 209 | Homo sapiens | Q99627 |
| Cullin-2 | O | protein | 745 | Homo sapiens | Q13617 |
| Elongin-B | P | protein | 105 | Homo sapiens | Q15370 |
| Eloc_human | Q | protein | 99 | Homo sapiens | Q03071 |
| RBX1_HUMAN | R | protein | 86 | Homo sapiens | P62877 |
| von Hippel-Lindau disease tumor suppressor | V | protein | 150 | Homo sapiens | P40337 |
1 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6R6H_1 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>6R6H_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>6R6H_3 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQF
Sequence of entity 4 (D), FASTA
>6R6H_4 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E), FASTA
>6R6H_5 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F), FASTA
>6R6H_6 COP9 signalosome complex subunit 6 (chains F)
MEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRSQEGRPVQVIGALIGKQEGR
NIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELEFLGWYTTGGPPDPSDIHVH
KQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEATMLFAELTYTLATEEAERIG
VDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILEYVKASEAGEVPFNHEILRE
AYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCNTMNQFVNKFNVLYDRQGIG
RRMRGLFF
Sequence of entity 7 (H), FASTA
>6R6H_7 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 8 (O), FASTA
>6R6H_8 Cullin-2 (chains O)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 9 (P), FASTA
>6R6H_9 Elongin-B (chains P)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKA
Sequence of entity 10 (Q), FASTA
>6R6H_10 ELOC_HUMAN (chains Q)
MSQDFVTLVSKDDKEYEISRSAAMISPTLKAMIEGPFRESKGRIELKQFDSHILEKAVEY
LNYNLKYSGVSEDDDEIPEFEIPTEMSLELLLAADYLSI
Sequence of entity 11 (R), FASTA
>6R6H_11 RBX1_HUMAN (chains R)
AKKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCN
HAFHFHCISRWLKTRQVCPLDNREWE
Sequence of entity 12 (V), FASTA
>6R6H_12 von Hippel-Lindau disease tumor suppressor (chains V)
RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLF
RDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLD
IVRSLYEDLEDHPNVQKDLERLTQERIAAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
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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