9EG1: COP9 signalosome complex subunit 2
COP9 signalosome deneddylation complex with cullin-5. Determined by electron microscopy at 3.52 Å resolution. Released 3 Dec 2025.
- Method
- Electron microscopy
- Resolution
- 3.52 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 23,752
- Mol. weight
- 441.25 kDa
- Ligands
- ZN
- Released
- 3 Dec 2025
Explore 9EG1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9EG1 contains 161 α-helices and 71 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: 25 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-49 | 5 | |
| α-helix | 54-66 | 13 | |
| α-helix | 71-82 | 12 | |
| α-helix | 89-101 | 13 | |
| α-helix | 128-132 | 5 | |
| α-helix | 133-137 | 5 | |
| α-helix | 138-155 | 18 | |
| α-helix | 158-175 | 18 | |
| α-helix | 178-188 | 11 | |
| α-helix | 189-191 | 3 | |
| α-helix | 195-212 | 18 | |
| α-helix | 215-227 | 13 | |
| α-helix | 244-259 | 16 | |
| α-helix | 263-270 | 8 | |
| α-helix | 286-300 | 15 | |
| α-helix | 303-306 | 4 | |
| α-helix | 307-311 | 5 | |
| α-helix | 314-316 | 3 | |
| α-helix | 317-322 | 6 | |
| α-helix | 324-334 | 11 | |
| α-helix | 338-352 | 15 | |
| α-helix | 363-378 | 16 | |
| β-strand | 381-385 | 5 | 1 |
| α-helix | 386-392 | 7 | |
| α-helix | 397-410 | 14 | |
| β-strand | 415-418 | 4 | 1 |
| β-strand | 423-426 | 4 | 1 |
| α-helix | 431-461 | 31 | |
Chain B: 22 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-80 | 16 | |
| α-helix | 85-102 | 18 | |
| α-helix | 108-117 | 10 | |
| α-helix | 118-120 | 3 | |
| α-helix | 125-138 | 14 | |
| α-helix | 145-155 | 11 | |
| α-helix | 164-167 | 4 | |
| α-helix | 168-171 | 4 | |
| α-helix | 172-179 | 8 | |
| α-helix | 191-207 | 17 | |
| α-helix | 211-221 | 11 | |
| α-helix | 233-248 | 16 | |
| α-helix | 251-267 | 17 | |
| α-helix | 276-285 | 10 | |
| α-helix | 300-304 | 5 | |
| α-helix | 309-318 | 10 | |
| α-helix | 324-332 | 9 | |
| α-helix | 343-346 | 4 | |
| α-helix | 353-362 | 10 | |
| 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: 25 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| α-helix | 21-28 | 8 | |
| α-helix | 37-42 | 6 | |
| α-helix | 43-46 | 4 | |
| α-helix | 54-63 | 10 | |
| α-helix | 74-87 | 14 | |
| α-helix | 92-96 | 5 | |
| α-helix | 99-113 | 15 | |
| α-helix | 123-129 | 7 | |
| β-strand | 137-138 | 2 | 17 |
| α-helix | 142-151 | 10 | |
| α-helix | 156-161 | 6 | |
| α-helix | 165-166 | 2 | |
| β-strand | 168-169 | 2 | 17 |
| α-helix | 178-194 | 17 | |
| α-helix | 198-209 | 12 | |
| α-helix | 218-234 | 17 | |
| α-helix | 238-242 | 5 | |
| α-helix | 249-253 | 5 | |
| α-helix | 254-256 | 3 | |
| α-helix | 259-266 | 8 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-310 | 17 | |
| β-strand | 314-318 | 5 | 1 |
| α-helix | 319-322 | 4 | |
| α-helix | 331-343 | 13 | |
| β-strand | 349-352 | 4 | 1 |
| β-strand | 357-360 | 4 | 1 |
| α-helix | 370-398 | 29 | |
Chain D: 24 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
| α-helix | 21-34 | 14 | |
| α-helix | 40-53 | 14 | |
| α-helix | 62-72 | 11 | |
| α-helix | 78-92 | 15 | |
| α-helix | 102-116 | 15 | |
| α-helix | 122-128 | 7 | |
| 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 | 237-238 | 2 | |
| α-helix | 240-251 | 12 | |
| α-helix | 253-257 | 5 | |
| α-helix | 261-268 | 8 | |
| α-helix | 271-273 | 3 | |
| α-helix | 279-284 | 6 | |
| α-helix | 287-289 | 3 | |
| β-strand | 292 | 1 | 2 |
| β-strand | 298 | 1 | 2 |
| α-helix | 300-312 | 13 | |
| β-strand | 316 | 1 | 3 |
| β-strand | 318-320 | 3 | 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, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-27 | 4 | |
| α-helix | 33-42 | 10 | |
| α-helix | 44-46 | 3 | |
| β-strand | 54-58 | 5 | 4 |
| α-helix | 59-72 | 14 | |
| β-strand | 78-86 | 9 | 4 |
| β-strand | 89-97 | 9 | 4 |
| β-strand | 107 | 1 | 5 |
| α-helix | 111-127 | 17 | |
| β-strand | 132-139 | 8 | 4 |
| α-helix | 149-161 | 13 | |
| β-strand | 166-170 | 5 | 4 |
| α-helix | 172-178 | 7 | |
| β-strand | 184-186 | 3 | 4 |
| β-strand | 188 | 1 | 6 |
| α-helix | 189-190 | 2 | |
| β-strand | 221 | 1 | 6 |
| β-strand | 225-229 | 5 | 4 |
| α-helix | 232-242 | 11 | |
| α-helix | 246-251 | 6 | |
| α-helix | 259-280 | 22 | |
| α-helix | 299-328 | 30 | |
Chain F: 8 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40-42 | 3 | 7 |
| α-helix | 47-62 | 16 | |
| β-strand | 69 | 1 | 7 |
| β-strand | 72-77 | 6 | 7 |
| β-strand | 80-85 | 6 | 7 |
| β-strand | 91-94 | 4 | 8 |
| β-strand | 97-100 | 4 | 8 |
| α-helix | 102-111 | 10 | |
| β-strand | 120-127 | 8 | 7 |
| α-helix | 133-145 | 13 | |
| β-strand | 150-154 | 5 | 7 |
| β-strand | 166-172 | 7 | 7 |
| α-helix | 180 | 1 | |
| β-strand | 181-185 | 5 | 7 |
| β-strand | 188-189 | 2 | 7 |
| α-helix | 194-206 | 13 | |
| α-helix | 216-247 | 32 | |
| α-helix | 256-265 | 10 | |
| α-helix | 273-312 | 40 | |
Chain G: 13 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-16 | 6 | |
| α-helix | 17-19 | 3 | |
| α-helix | 25-36 | 12 | |
| α-helix | 45-48 | 4 | |
| α-helix | 50-53 | 4 | |
| α-helix | 54-56 | 3 | |
| α-helix | 61-71 | 11 | |
| α-helix | 77-80 | 4 | |
| α-helix | 86-87 | 2 | |
| α-helix | 90-107 | 18 | |
| β-strand | 110-112 | 3 | 3 |
| α-helix | 113-120 | 8 | |
| α-helix | 125-138 | 14 | |
| β-strand | 141-146 | 6 | 3 |
| β-strand | 151-157 | 7 | 3 |
| α-helix | 167-220 | 54 | |
Chain H: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-25 | 13 | |
| α-helix | 34-46 | 13 | |
| α-helix | 50-59 | 10 | |
| α-helix | 62-67 | 6 | |
| α-helix | 70-82 | 13 | |
| α-helix | 86-93 | 8 | |
| α-helix | 100-102 | 3 | |
| α-helix | 103-124 | 22 | |
| β-strand | 125-127 | 3 | 1 |
| β-strand | 128-129 | 2 | 9 |
| α-helix | 130-137 | 8 | |
| α-helix | 143-150 | 8 | |
| β-strand | 154-156 | 3 | 9 |
| β-strand | 161-163 | 3 | 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 2 | B | protein | 443 | Homo sapiens | P61201 (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 (AlphaFold model) |
| COP9 signalosome complex subunit 6 | F | protein | 327 | Homo sapiens | Q7L5N1 (AlphaFold model) |
| COP9 signalosome complex subunit 7b | G | protein | 264 | Homo sapiens | Q9H9Q2 |
| COP9 signalosome complex subunit 8 | H | protein | 209 | Homo sapiens | Q99627 |
| Cullin-5 | J | protein | 780 | Homo sapiens | Q93034 |
| RING-box protein 2 | K | protein | 113 | Homo sapiens | Q9UBF6 |
| COP9 signalosome complex subunit 1 | A | protein | 491 | Homo sapiens | Q13098 |
| COP9 signalosome complex subunit 3 | C | protein | 423 | Homo sapiens | Q9UNS2 |
| NEDD8 | I | protein | 81 | Homo sapiens | Q15843 |
Sequence of entity 1 (B), FASTA
>9EG1_1 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 2 (D), FASTA
>9EG1_2 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 3 (E), FASTA
>9EG1_3 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLAVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGINVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 4 (F), FASTA
>9EG1_4 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 5 (G), FASTA
>9EG1_5 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 6 (H), FASTA
>9EG1_6 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 7 (J), FASTA
>9EG1_7 Cullin-5 (chains J)
MATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAK
IHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMG
KQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGV
RESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKE
EEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLM
DKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQ
DDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLRKTP
LSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMVEWL
REVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSS
EKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQL
AVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDF
TEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQEAII
QIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA
Sequence of entity 8 (K), FASTA
>9EG1_8 RING-box protein 2 (chains K)
MADVEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDA
CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK
Sequence of entity 9 (A), FASTA
>9EG1_9 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 10 (C), FASTA
>9EG1_10 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 11 (I), FASTA
>9EG1_11 NEDD8 (chains I)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGGGGLRQ
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 P61201 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6A73 2.45 Å, Complex structure of CSN2 with IP6
- 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
Browse structure collections
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