9EFV: CSN-N8CUL1
Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3. Determined by electron microscopy at 3.03 Å resolution. Released 3 Dec 2025.
- Method
- Electron microscopy
- Resolution
- 3.03 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 24,947
- Mol. weight
- 440.19 kDa
- Ligands
- ZN, 6LT
- Released
- 3 Dec 2025
Explore 9EFV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9EFV contains 173 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: 27 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-48 | 5 | |
| α-helix | 55-63 | 9 | |
| α-helix | 71-78 | 8 | |
| α-helix | 84-86 | 3 | |
| α-helix | 91-101 | 11 | |
| α-helix | 130-138 | 9 | |
| α-helix | 141-144 | 4 | |
| α-helix | 147-155 | 9 | |
| α-helix | 158-175 | 18 | |
| α-helix | 178-188 | 11 | |
| α-helix | 195-211 | 17 | |
| α-helix | 216-227 | 12 | |
| α-helix | 230-233 | 4 | |
| α-helix | 245-259 | 15 | |
| α-helix | 263-271 | 9 | |
| α-helix | 275-277 | 3 | |
| α-helix | 289-300 | 12 | |
| α-helix | 303-306 | 4 | |
| α-helix | 307-311 | 5 | |
| α-helix | 314-322 | 9 | |
| 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 | 397-410 | 14 | |
| 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 | 50-60 | 11 | |
| α-helix | 67-79 | 13 | |
| α-helix | 85-92 | 8 | |
| α-helix | 97-101 | 5 | |
| α-helix | 105-118 | 14 | |
| α-helix | 120-122 | 3 | |
| α-helix | 125-142 | 18 | |
| α-helix | 147-161 | 15 | |
| α-helix | 168-176 | 9 | |
| α-helix | 191-207 | 17 | |
| α-helix | 212-222 | 11 | |
| α-helix | 233-235 | 3 | |
| α-helix | 237-248 | 12 | |
| α-helix | 251-267 | 17 | |
| α-helix | 273-286 | 14 | |
| α-helix | 293-295 | 3 | |
| 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: 25 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-18 | 15 | |
| α-helix | 22-29 | 8 | |
| α-helix | 32-36 | 5 | |
| α-helix | 44-48 | 5 | |
| α-helix | 55-66 | 12 | |
| α-helix | 75-86 | 12 | |
| α-helix | 93-96 | 4 | |
| α-helix | 97-113 | 17 | |
| α-helix | 121-129 | 9 | |
| β-strand | 138 | 1 | 3 |
| α-helix | 141-151 | 11 | |
| α-helix | 159-161 | 3 | |
| β-strand | 169 | 1 | 3 |
| α-helix | 172-174 | 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 | 249-253 | 5 | |
| α-helix | 254-256 | 3 | |
| α-helix | 259-268 | 10 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-288 | 6 | |
| α-helix | 294-310 | 17 | |
| 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 | |
Chain D: 26 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-33 | 13 | |
| α-helix | 40-53 | 14 | |
| α-helix | 63-71 | 9 | |
| α-helix | 73-75 | 3 | |
| α-helix | 78-92 | 15 | |
| α-helix | 93-95 | 3 | |
| 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 | 237-238 | 2 | |
| α-helix | 240-251 | 12 | |
| α-helix | 253-257 | 5 | |
| α-helix | 261-268 | 8 | |
| α-helix | 271-273 | 3 | |
| α-helix | 275-277 | 3 | |
| α-helix | 281-284 | 4 | |
| α-helix | 287-290 | 4 | |
| β-strand | 292 | 1 | 4 |
| β-strand | 298 | 1 | 4 |
| α-helix | 300-315 | 16 | |
| β-strand | 316 | 1 | 5 |
| β-strand | 318-320 | 3 | 1 |
| α-helix | 321-327 | 7 | |
| α-helix | 335-342 | 8 | |
| β-strand | 351-353 | 3 | 1 |
| β-strand | 358-360 | 3 | 1 |
| α-helix | 367-391 | 25 | |
| α-helix | 393-404 | 12 | |
Chain E: 14 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-42 | 10 | |
| β-strand | 54-56 | 3 | 6 |
| α-helix | 59-70 | 12 | |
| β-strand | 78-86 | 9 | 6 |
| β-strand | 89-97 | 9 | 6 |
| α-helix | 115-121 | 7 | |
| α-helix | 123-126 | 4 | |
| β-strand | 135-138 | 4 | 6 |
| α-helix | 149-161 | 13 | |
| β-strand | 166-168 | 3 | 6 |
| α-helix | 172-178 | 7 | |
| β-strand | 185 | 1 | 6 |
| α-helix | 187 | 1 | |
| β-strand | 188 | 1 | 7 |
| α-helix | 189-190 | 2 | |
| α-helix | 211-216 | 6 | |
| β-strand | 221 | 1 | 7 |
| β-strand | 225-226 | 2 | 6 |
| α-helix | 234-238 | 5 | |
| α-helix | 240-243 | 4 | |
| α-helix | 259-280 | 22 | |
| α-helix | 299-324 | 26 | |
| α-helix | 325-329 | 5 | |
Chain F: 8 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 42 | 1 | 8 |
| α-helix | 45-62 | 18 | |
| β-strand | 69 | 1 | 9 |
| β-strand | 71-74 | 4 | 10 |
| β-strand | 83-87 | 5 | 10 |
| β-strand | 94 | 1 | 11 |
| β-strand | 97 | 1 | 11 |
| α-helix | 102-115 | 14 | |
| β-strand | 120-121 | 2 | 10 |
| β-strand | 123-127 | 5 | 9 |
| α-helix | 133-143 | 11 | |
| β-strand | 150-154 | 5 | 9 |
| α-helix | 163-164 | 2 | |
| β-strand | 167 | 1 | 9 |
| β-strand | 189 | 1 | 8 |
| α-helix | 194-203 | 10 | |
| α-helix | 216-247 | 32 | |
| α-helix | 256-265 | 10 | |
| α-helix | 273-310 | 38 | |
Chain G: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 25-36 | 12 | |
| α-helix | 50-53 | 4 | |
| α-helix | 54-56 | 3 | |
| 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 | 5 |
| α-helix | 113-120 | 8 | |
| α-helix | 125-137 | 13 | |
| β-strand | 141-146 | 6 | 5 |
| β-strand | 151-157 | 7 | 5 |
| 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 | 69-82 | 14 | |
| α-helix | 86-95 | 10 | |
| α-helix | 97-99 | 3 | |
| α-helix | 103-124 | 22 | |
| β-strand | 125-127 | 3 | 1 |
| β-strand | 128-129 | 2 | 12 |
| α-helix | 130-137 | 8 | |
| α-helix | 141-150 | 10 | |
| β-strand | 154-156 | 3 | 12 |
| β-strand | 161-163 | 3 | 12 |
| 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
>9EFV_1 COP9 signalosome complex subunit 1 (chains A)
MPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERL
QFIADHCPTLRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRSSLRELQNAPDAIPESG
VEPPALDTAWVEATRKKALLKLEKLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSN
ALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDS
QTQAILTKLKCAAGLAELAARKYKQAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALAT
FDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAP
HVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLILEGLISARVDSH
SKILYARDVDQRSTTFEKSLLMGKEFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTP
ANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>9EFV_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>9EFV_3 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 4 (D), FASTA
>9EFV_4 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E), FASTA
>9EFV_5 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F), FASTA
>9EFV_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>9EFV_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 8 (H), FASTA
>9EFV_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (I), FASTA
>9EFV_9 NEDD8 (chains I)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGGGGLRQ
Sequence of entity 10 (J), FASTA
>9EFV_10 Cullin-1 (chains J)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 11 (K), FASTA
>9EFV_11 E3 ubiquitin-protein ligase RBX1 (chains K)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
| 6LT | 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]… | C28 H29 F2 N5 O2 | 1 |
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
- 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
- 9EG1 3.52 Å, COP9 signalosome deneddylation complex with cullin-5
Browse structure collections
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