8H3F: KBTBD2-CRL3-CSN complex
Cryo-EM Structure of the KBTBD2-CRL3-CSN complex. Determined by electron microscopy at 6.73 Å resolution. Released 11 Oct 2023.
- Method
- Electron microscopy
- Resolution
- 6.73 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 36,711
- Mol. weight
- 578.45 kDa
- Ligands
- ZN
- Released
- 11 Oct 2023
Explore 8H3F in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8H3F contains 205 α-helices and 124 β-strands across 12 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, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 84-90 | 7 | |
| α-helix | 94-106 | 13 | |
| α-helix | 111-122 | 12 | |
| α-helix | 129-145 | 17 | |
| α-helix | 165-189 | 25 | |
| α-helix | 194-211 | 18 | |
| α-helix | 214-224 | 11 | |
| α-helix | 231-247 | 17 | |
| α-helix | 251-263 | 13 | |
| α-helix | 281-295 | 15 | |
| α-helix | 300-307 | 8 | |
| α-helix | 311-313 | 3 | |
| α-helix | 322-336 | 15 | |
| α-helix | 339-349 | 11 | |
| α-helix | 352-358 | 7 | |
| α-helix | 360-370 | 11 | |
| α-helix | 374-387 | 14 | |
| α-helix | 395-414 | 20 | |
| β-strand | 417 | 1 | 2 |
| β-strand | 419-421 | 3 | 3 |
| α-helix | 422-427 | 6 | |
| α-helix | 433-446 | 14 | |
| β-strand | 451-454 | 4 | 3 |
| β-strand | 459-462 | 4 | 3 |
| α-helix | 463 | 1 | |
| α-helix | 467-497 | 31 | |
| β-strand | 502 | 1 | 4 |
Chain B: 20 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-44 | 14 | |
| α-helix | 50-59 | 10 | |
| α-helix | 66-81 | 16 | |
| α-helix | 86-101 | 16 | |
| α-helix | 108-119 | 12 | |
| α-helix | 125-141 | 17 | |
| α-helix | 145-161 | 17 | |
| α-helix | 166-179 | 14 | |
| β-strand | 181 | 1 | 5 |
| β-strand | 184 | 1 | 5 |
| α-helix | 191-208 | 18 | |
| α-helix | 211-224 | 14 | |
| α-helix | 231-248 | 18 | |
| α-helix | 251-268 | 18 | |
| α-helix | 272-286 | 15 | |
| α-helix | 306-320 | 15 | |
| α-helix | 323-332 | 10 | |
| α-helix | 334-337 | 4 | |
| α-helix | 341-362 | 22 | |
| β-strand | 367 | 1 | 6 |
| β-strand | 369-370 | 2 | 2 |
| α-helix | 371-378 | 8 | |
| α-helix | 382-394 | 13 | |
| β-strand | 400-403 | 4 | 2 |
| β-strand | 408-411 | 4 | 2 |
| α-helix | 421-442 | 22 | |
Chain C: 23 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-17 | 15 | |
| α-helix | 21-28 | 8 | |
| α-helix | 33-37 | 5 | |
| α-helix | 42-48 | 7 | |
| α-helix | 53-66 | 14 | |
| α-helix | 74-86 | 13 | |
| α-helix | 97-114 | 18 | |
| α-helix | 120-131 | 12 | |
| β-strand | 138 | 1 | 7 |
| α-helix | 141-152 | 12 | |
| α-helix | 158-162 | 5 | |
| β-strand | 169 | 1 | 7 |
| α-helix | 178-194 | 17 | |
| α-helix | 198-209 | 12 | |
| β-strand | 213 | 1 | 4 |
| α-helix | 218-234 | 17 | |
| α-helix | 239-241 | 3 | |
| α-helix | 249-256 | 8 | |
| α-helix | 258-269 | 12 | |
| α-helix | 272-281 | 10 | |
| α-helix | 283-287 | 5 | |
| α-helix | 293-311 | 19 | |
| β-strand | 314-318 | 5 | 3 |
| α-helix | 319-325 | 7 | |
| α-helix | 331-343 | 13 | |
| β-strand | 349-352 | 4 | 3 |
| β-strand | 357-360 | 4 | 3 |
| α-helix | 370-398 | 29 | |
| α-helix | 401-407 | 7 | |
Chain D: 24 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-13 | 12 | |
| α-helix | 19-35 | 17 | |
| α-helix | 38-53 | 16 | |
| α-helix | 59-72 | 14 | |
| α-helix | 73-75 | 3 | |
| α-helix | 80-82 | 3 | |
| α-helix | 83-91 | 9 | |
| α-helix | 101-116 | 16 | |
| α-helix | 120-128 | 9 | |
| α-helix | 141-158 | 18 | |
| α-helix | 162-173 | 12 | |
| α-helix | 175-177 | 3 | |
| α-helix | 181-198 | 18 | |
| α-helix | 201-212 | 12 | |
| α-helix | 219-235 | 17 | |
| α-helix | 240-249 | 10 | |
| α-helix | 253-257 | 5 | |
| α-helix | 261-268 | 8 | |
| α-helix | 277-285 | 9 | |
| α-helix | 299-315 | 17 | |
| β-strand | 318-320 | 3 | 6 |
| α-helix | 321-328 | 8 | |
| α-helix | 332-345 | 14 | |
| β-strand | 351-353 | 3 | 6 |
| β-strand | 358-360 | 3 | 6 |
| α-helix | 367-391 | 25 | |
| α-helix | 393-405 | 13 | |
Chain E: 15 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 33-42 | 10 | |
| α-helix | 44-47 | 4 | |
| β-strand | 54-57 | 4 | 1 |
| α-helix | 59-72 | 14 | |
| β-strand | 78-86 | 9 | 1 |
| β-strand | 89-97 | 9 | 1 |
| α-helix | 109-113 | 5 | |
| α-helix | 114-126 | 13 | |
| β-strand | 132-139 | 8 | 1 |
| α-helix | 149-158 | 10 | |
| β-strand | 166-170 | 5 | 1 |
| α-helix | 172-178 | 7 | |
| β-strand | 183-187 | 5 | 1 |
| α-helix | 188-190 | 3 | |
| α-helix | 193-195 | 3 | |
| α-helix | 208-220 | 13 | |
| β-strand | 222-223 | 2 | 1 |
| β-strand | 225-226 | 2 | 1 |
| α-helix | 232-244 | 13 | |
| α-helix | 255-257 | 3 | |
| α-helix | 261-283 | 23 | |
| α-helix | 290-329 | 40 | |
Chain F: 8 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31 | 1 | 8 |
| α-helix | 35-37 | 3 | |
| β-strand | 40-43 | 4 | 8 |
| α-helix | 45-61 | 17 | |
| β-strand | 69-77 | 9 | 8 |
| β-strand | 80-88 | 9 | 8 |
| β-strand | 91-94 | 4 | 9 |
| β-strand | 97-100 | 4 | 9 |
| α-helix | 102-113 | 12 | |
| β-strand | 120-127 | 8 | 8 |
| α-helix | 135-145 | 11 | |
| β-strand | 150-154 | 5 | 8 |
| β-strand | 165-175 | 11 | 8 |
| β-strand | 178-186 | 9 | 8 |
| β-strand | 189-190 | 2 | 8 |
| α-helix | 194-207 | 14 | |
| α-helix | 217-247 | 31 | |
| α-helix | 255-265 | 11 | |
| α-helix | 273-312 | 40 | |
Chain G: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-19 | 12 | |
| α-helix | 25-36 | 12 | |
| α-helix | 44-47 | 4 | |
| α-helix | 50-57 | 8 | |
| α-helix | 62-72 | 11 | |
| α-helix | 75-80 | 6 | |
| α-helix | 86-88 | 3 | |
| α-helix | 90-107 | 18 | |
| β-strand | 110-112 | 3 | 6 |
| α-helix | 113-119 | 7 | |
| α-helix | 125-137 | 13 | |
| β-strand | 141-146 | 6 | 6 |
| β-strand | 151-157 | 7 | 6 |
| α-helix | 167-219 | 53 | |
Chain H: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-25 | 15 | |
| α-helix | 34-46 | 13 | |
| α-helix | 50-59 | 10 | |
| α-helix | 62-67 | 6 | |
| α-helix | 69-83 | 15 | |
| α-helix | 86-93 | 8 | |
| α-helix | 97-99 | 3 | |
| α-helix | 103-124 | 22 | |
| β-strand | 125-127 | 3 | 3 |
| β-strand | 128-129 | 2 | 10 |
| α-helix | 130-137 | 8 | |
| α-helix | 141-149 | 9 | |
| β-strand | 154-156 | 3 | 10 |
| β-strand | 161-163 | 3 | 10 |
| α-helix | 193-208 | 16 | |
4 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 5 | E | protein | 334 | Homo sapiens | Q92905 (AlphaFold model) |
| COP9 signalosome complex subunit 1 | A | protein | 527 | 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 | 441 | Homo sapiens | Q9UNS2 (AlphaFold model) |
| COP9 signalosome complex subunit 4 | D | protein | 406 | Homo sapiens | Q9BT78 |
| COP9 signalosome complex subunit 6 | F | protein | 327 | Homo sapiens | Q7L5N1 |
| COP9 signalosome complex subunit 7b | G | protein | 220 | Homo sapiens | Q9H9Q2 |
| COP9 signalosome complex subunit 8 | H | protein | 209 | Homo sapiens | Q99627 |
| Kelch repeat and BTB domain-containing protein 2 | I, M | protein | 636 | Homo sapiens | Q8IY47 |
| E3 ubiquitin-protein ligase RBX1 | R | protein | 121 | Homo sapiens | P62877 |
| Cullin-3 | L | protein | 768 | Homo sapiens | Q13618 |
Sequence of entity 1 (E), FASTA
>8H3F_1 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 2 (A), FASTA
>8H3F_2 COP9 signalosome complex subunit 1 (chains A)
MRDSSAPSSASSSVTDLYCTPHSSRSDLVLPGTAGDFSLSASLSACTLLYEGAVEPMQID
VDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERLQFIADHCPTLRVEALKMALS
FVQRTFNVDMYEEIHRKLSEATRELQNAPDAIPESGVEPPALDTAWVEATRKKALLKLEK
LDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDYCTSAKHVINMCLN
VIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKCAAGLAELAARKYK
QAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALATFDRQELQRNVISSSSFKLFLELEP
QVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAPHVRTLYTQIRNRALIQYFSPYVSA
DMHRMAAAFNTTVAALEDELTQLILEGLISARVDSHSKILYARDVDQRSTTFEKSLLMGK
EFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM
Sequence of entity 3 (B), FASTA
>8H3F_3 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 4 (C), FASTA
>8H3F_4 COP9 signalosome complex subunit 3 (chains C)
WSHPQFEKLEVLFQGPGSMASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHL
DTVLGALDVQEHSLGVLAVLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAG
LCHQLTNALVERKQPLRGIGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYL
DVDMMDICKENGAYDAKHFLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLE
SYKKYILVSLILLGKVQQLPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKH
SETFTRDNNMGLVKQCLSSLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMI
EDGEIFASINQKDGMVSFHDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQ
FVQKSMGSQEDDSGNKPSSYS
Sequence of entity 5 (D), FASTA
>8H3F_5 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 6 (F), FASTA
>8H3F_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>8H3F_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTL
Sequence of entity 8 (H), FASTA
>8H3F_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (I, M), FASTA
>8H3F_9 Kelch repeat and BTB domain-containing protein 2 (chains I, M)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKDMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPVENLYFQGHHHHHH
Sequence of entity 10 (R), FASTA
>8H3F_10 E3 ubiquitin-protein ligase RBX1 (chains R)
HHHHHHENLYFQGMAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRN
HIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG
H
Sequence of entity 11 (L), FASTA
>8H3F_11 Cullin-3 (chains L)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3 KBTBD2. Hu, Y., Zhang, Z., Mao, Q. et al. Nat Struct Mol Biol (2024) 31:336-350. DOI 10.1038/s41594-023-01182-6 · PubMed
Other PDB entries of the same protein (UniProt Q92905 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5JOH 1.99 Å, Crystal structure of CSN5(2-257) in complex with CNS5i-1b
- 5M5Q 2.2 Å, COPS5(2-257) in complex with a azaindole (compound 4)
- 5JOG 2.46 Å, Crystal structure of CSN5(2-257) in complex with CNS5i-3
- 4F7O 2.6 Å, Crystal structure of CSN5
- 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…
Browse structure collections
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