9EFM: COP9 signalosome complex subunit 1
Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1. Determined by electron microscopy at 3.16 Å resolution. Released 3 Dec 2025.
- Method
- Electron microscopy
- Resolution
- 3.16 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 24,951
- Mol. weight
- 439.56 kDa
- Ligands
- ZN
- Released
- 3 Dec 2025
Explore 9EFM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9EFM contains 168 α-helices and 69 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: 27 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-48 | 5 | |
| α-helix | 53-56 | 4 | |
| α-helix | 57-60 | 4 | |
| α-helix | 63-65 | 3 | |
| α-helix | 71-78 | 8 | |
| α-helix | 90-93 | 4 | |
| α-helix | 95-99 | 5 | |
| α-helix | 130-154 | 25 | |
| α-helix | 162-175 | 14 | |
| α-helix | 179-190 | 12 | |
| α-helix | 195-212 | 18 | |
| α-helix | 215-227 | 13 | |
| α-helix | 230-236 | 7 | |
| α-helix | 245-259 | 15 | |
| α-helix | 263-268 | 6 | |
| α-helix | 275-277 | 3 | |
| α-helix | 287-300 | 14 | |
| α-helix | 303-306 | 4 | |
| α-helix | 307-311 | 5 | |
| α-helix | 317-322 | 6 | |
| α-helix | 324-334 | 11 | |
| α-helix | 338-352 | 15 | |
| α-helix | 359-378 | 20 | |
| β-strand | 381-385 | 5 | 1 |
| α-helix | 386-392 | 7 | |
| α-helix | 397-409 | 13 | |
| β-strand | 415-418 | 4 | 1 |
| β-strand | 423-426 | 4 | 1 |
| α-helix | 427 | 1 | |
| α-helix | 431-461 | 31 | |
| β-strand | 466 | 1 | 2 |
Chain B: 25 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-41 | 12 | |
| α-helix | 51-60 | 10 | |
| α-helix | 66-81 | 16 | |
| α-helix | 85-95 | 11 | |
| α-helix | 105-118 | 14 | |
| α-helix | 120-122 | 3 | |
| α-helix | 125-142 | 18 | |
| α-helix | 146-161 | 16 | |
| α-helix | 168-176 | 9 | |
| α-helix | 191-207 | 17 | |
| α-helix | 211-222 | 12 | |
| α-helix | 233-235 | 3 | |
| α-helix | 237-248 | 12 | |
| α-helix | 252-267 | 16 | |
| α-helix | 273-285 | 13 | |
| α-helix | 293-295 | 3 | |
| α-helix | 301-304 | 4 | |
| α-helix | 309-318 | 10 | |
| α-helix | 323-332 | 10 | |
| α-helix | 341-344 | 4 | |
| α-helix | 345-347 | 3 | |
| 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: 26 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| α-helix | 21-28 | 8 | |
| α-helix | 37-39 | 3 | |
| α-helix | 40-46 | 7 | |
| α-helix | 54-62 | 9 | |
| α-helix | 74-87 | 14 | |
| α-helix | 94-96 | 3 | |
| α-helix | 99-113 | 15 | |
| α-helix | 127-131 | 5 | |
| β-strand | 137-138 | 2 | 3 |
| α-helix | 142-151 | 10 | |
| α-helix | 156-161 | 6 | |
| β-strand | 168-169 | 2 | 3 |
| α-helix | 178-194 | 17 | |
| α-helix | 198-209 | 12 | |
| 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 | 259-266 | 8 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 296-310 | 15 | |
| β-strand | 314-318 | 5 | 1 |
| α-helix | 319-325 | 7 | |
| α-helix | 331-344 | 14 | |
| β-strand | 349-352 | 4 | 1 |
| β-strand | 357-360 | 4 | 1 |
| α-helix | 370-398 | 29 | |
| α-helix | 401-405 | 5 | |
Chain D: 25 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-13 | 8 | |
| α-helix | 20-23 | 4 | |
| α-helix | 25-33 | 9 | |
| α-helix | 39-50 | 12 | |
| α-helix | 62-70 | 9 | |
| α-helix | 78-92 | 15 | |
| α-helix | 93-95 | 3 | |
| α-helix | 102-116 | 15 | |
| α-helix | 120-129 | 10 | |
| α-helix | 141-157 | 17 | |
| α-helix | 161-171 | 11 | |
| α-helix | 181-197 | 17 | |
| α-helix | 201-211 | 11 | |
| α-helix | 219-235 | 17 | |
| α-helix | 240-251 | 12 | |
| α-helix | 253-257 | 5 | |
| α-helix | 261-268 | 8 | |
| α-helix | 271-274 | 4 | |
| α-helix | 279-282 | 4 | |
| α-helix | 287-290 | 4 | |
| α-helix | 300-312 | 13 | |
| β-strand | 316 | 1 | 4 |
| β-strand | 318-320 | 3 | 1 |
| α-helix | 321-327 | 7 | |
| α-helix | 334-342 | 9 | |
| β-strand | 351-353 | 3 | 1 |
| β-strand | 358-360 | 3 | 1 |
| α-helix | 367-391 | 25 | |
| α-helix | 393-402 | 10 | |
Chain E: 16 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-17 | 8 | |
| α-helix | 26-29 | 4 | |
| α-helix | 33-42 | 10 | |
| β-strand | 54-58 | 5 | 5 |
| α-helix | 59-71 | 13 | |
| β-strand | 78-86 | 9 | 5 |
| β-strand | 89-92 | 4 | 5 |
| β-strand | 96-97 | 2 | 5 |
| β-strand | 102 | 1 | 6 |
| β-strand | 107 | 1 | 6 |
| α-helix | 113-126 | 14 | |
| β-strand | 132-139 | 8 | 5 |
| α-helix | 149-161 | 13 | |
| β-strand | 166-170 | 5 | 5 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-188 | 6 | 5 |
| α-helix | 189-190 | 2 | |
| α-helix | 206-213 | 8 | |
| α-helix | 218-220 | 3 | |
| β-strand | 221-223 | 3 | 5 |
| α-helix | 224 | 1 | |
| β-strand | 225-229 | 5 | 5 |
| α-helix | 232-239 | 8 | |
| α-helix | 247-250 | 4 | |
| α-helix | 259-281 | 23 | |
| α-helix | 299-324 | 26 | |
| α-helix | 325-329 | 5 | |
Chain F: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40-43 | 4 | 7 |
| α-helix | 47-62 | 16 | |
| β-strand | 69-77 | 9 | 7 |
| β-strand | 80-88 | 9 | 7 |
| β-strand | 91-94 | 4 | 8 |
| β-strand | 97-100 | 4 | 8 |
| α-helix | 102-113 | 12 | |
| β-strand | 120-127 | 8 | 7 |
| α-helix | 133-143 | 11 | |
| β-strand | 150-154 | 5 | 7 |
| β-strand | 166-172 | 7 | 7 |
| β-strand | 181-185 | 5 | 7 |
| β-strand | 188-189 | 2 | 7 |
| α-helix | 194-205 | 12 | |
| α-helix | 217-247 | 31 | |
| α-helix | 254-265 | 12 | |
| α-helix | 273-310 | 38 | |
Chain G: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-18 | 8 | |
| α-helix | 25-36 | 12 | |
| α-helix | 45-47 | 3 | |
| α-helix | 50-53 | 4 | |
| α-helix | 61-71 | 11 | |
| α-helix | 76-80 | 5 | |
| α-helix | 86-87 | 2 | |
| α-helix | 90-107 | 18 | |
| β-strand | 110-112 | 3 | 4 |
| α-helix | 113-119 | 7 | |
| α-helix | 125-137 | 13 | |
| β-strand | 141-146 | 6 | 4 |
| β-strand | 151-157 | 7 | 4 |
| α-helix | 167-219 | 53 | |
Chain H: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-25 | 14 | |
| α-helix | 34-46 | 13 | |
| α-helix | 50-59 | 10 | |
| α-helix | 62-67 | 6 | |
| α-helix | 69-82 | 14 | |
| α-helix | 86-95 | 10 | |
| α-helix | 103-124 | 22 | |
| β-strand | 125-127 | 3 | 1 |
| β-strand | 128-129 | 2 | 9 |
| α-helix | 130-137 | 8 | |
| α-helix | 143-149 | 7 | |
| β-strand | 155-156 | 2 | 9 |
| β-strand | 161-162 | 2 | 9 |
| α-helix | 196-207 | 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 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 | 423 | 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 | 327 | Homo sapiens | Q7L5N1 |
| COP9 signalosome complex subunit 7b | G | protein | 264 | Homo sapiens | Q9H9Q2 |
| COP9 signalosome complex subunit 8 | H | protein | 209 | Homo sapiens | Q99627 |
| NEDD8 | I | protein | 81 | Homo sapiens | Q15843 |
| Cullin-1 | J | protein | 776 | Homo sapiens | Q13616 |
| E3 ubiquitin-protein ligase RBX1 | K | protein | 108 | Homo sapiens | P62877 |
Sequence of entity 1 (A), FASTA
>9EFM_1 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>9EFM_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>9EFM_3 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 4 (D), FASTA
>9EFM_4 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E), FASTA
>9EFM_5 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLAVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGINVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F), FASTA
>9EFM_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>9EFM_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 8 (H), FASTA
>9EFM_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (I), FASTA
>9EFM_9 NEDD8 (chains I)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGGGGLRQ
Sequence of entity 10 (J), FASTA
>9EFM_10 Cullin-1 (chains J)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 11 (K), FASTA
>9EFM_11 E3 ubiquitin-protein ligase RBX1 (chains K)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
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 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
- 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
- 9EG1 3.52 Å, COP9 signalosome deneddylation complex with cullin-5
Browse structure collections
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