8H38: KBTBD2-CRL3~N8-CSN(mutate) complex

Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex. Determined by electron microscopy at 4.25 Å resolution. Released 11 Oct 2023.

Method
Electron microscopy
Resolution
4.25 Å
Organism
Homo sapiens
Chains
13
Atoms
37,306
Mol. weight
584.69 kDa
Ligands
ZN
Released
11 Oct 2023

Explore 8H38 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H38 contains 218 α-helices and 136 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, 4 β-strands

ElementResiduesLengthSheet
α-helix84-907
α-helix94-10613
α-helix111-12212
α-helix129-14517
α-helix165-19127
α-helix194-21118
α-helix214-22411
α-helix231-24717
α-helix251-26313
α-helix281-29515
α-helix300-3078
α-helix311-3133
α-helix322-33615
α-helix339-34911
α-helix352-3587
α-helix360-37011
α-helix374-38815
α-helix395-41420
β-strand417-42151
α-helix422-4276
α-helix433-44614
β-strand451-45441
β-strand459-46241
α-helix4631
α-helix467-49731
β-strand50212
Chain B: 21 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix31-4111
α-helix47-6115
α-helix66-8116
α-helix86-9914
α-helix105-11915
α-helix125-14117
α-helix145-16117
α-helix166-17712
α-helix191-20818
α-helix211-22414
α-helix231-24818
α-helix251-26818
α-helix273-28614
α-helix301-3044
α-helix306-32015
α-helix323-33210
α-helix334-3374
α-helix341-36626
β-strand369-37021
α-helix371-3788
α-helix382-39413
β-strand40013
β-strand402-40321
β-strand408-40921
β-strand41113
α-helix421-44222
Chain C: 22 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix3-1715
α-helix21-288
α-helix33-375
α-helix42-487
α-helix53-6715
α-helix74-8613
α-helix97-11418
α-helix118-13114
β-strand13814
α-helix141-15212
α-helix158-1625
β-strand16914
α-helix178-19417
α-helix198-20912
β-strand21312
α-helix218-23417
α-helix239-2413
α-helix249-2568
α-helix258-26912
α-helix272-28110
α-helix293-31321
β-strand314-31851
α-helix319-3268
α-helix331-34313
β-strand349-35241
β-strand357-36041
α-helix370-39930
α-helix401-4077
Chain D: 23 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix2-1312
α-helix19-3517
α-helix38-5316
α-helix59-7214
α-helix73-753
α-helix80-823
α-helix83-919
α-helix101-11616
α-helix120-1289
α-helix141-15717
α-helix163-17513
α-helix181-19717
α-helix201-21212
α-helix219-23517
α-helix240-24910
α-helix253-2575
α-helix261-2699
α-helix278-2858
α-helix299-31517
β-strand316-31835
β-strand319-32026
α-helix321-3288
α-helix332-34514
β-strand35117
β-strand358-35926
β-strand36017
α-helix367-39125
α-helix393-40513
Chain E: 14 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix27-293
α-helix33-4210
α-helix44-474
β-strand54-5748
α-helix59-7113
β-strand78-8698
β-strand89-9688
α-helix113-12715
β-strand132-13988
α-helix149-16113
β-strand166-17168
α-helix172-1787
β-strand182-18878
α-helix189-1902
α-helix193-1964
α-helix208-21710
β-strand221-22338
β-strand225-22738
α-helix232-24615
α-helix255-2573
α-helix259-28325
α-helix290-32940
Chain F: 8 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand3119
α-helix35-373
β-strand40-4349
α-helix45-6117
β-strand69-7799
β-strand80-8899
β-strand91-94410
β-strand97-100410
α-helix102-11312
β-strand120-12789
α-helix135-1439
β-strand150-15459
β-strand165-175119
β-strand178-18699
β-strand189-19029
α-helix194-20815
α-helix218-24730
α-helix255-26410
α-helix273-31240
Chain G: 11 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix8-1912
α-helix25-3612
α-helix44-474
α-helix50-578
α-helix62-7211
α-helix75-806
α-helix86-883
α-helix90-10718
β-strand110-11235
α-helix113-1197
α-helix125-13713
β-strand141-14665
β-strand151-15775
α-helix166-21954
Chain H: 11 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix11-2515
α-helix34-4613
α-helix50-5910
α-helix62-676
α-helix69-8315
α-helix86-9510
α-helix97-993
α-helix103-12422
β-strand125-12731
β-strand128-129211
α-helix130-1378
α-helix141-1499
β-strand154-156311
β-strand161-163311
α-helix193-20816

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
COP9 signalosome complex subunit 1Aprotein527Homo sapiensQ13098 (AlphaFold model)
COP9 signalosome complex subunit 2Bprotein443Homo sapiensP61201 (AlphaFold model)
COP9 signalosome complex subunit 3Cprotein423Homo sapiensQ9UNS2 (AlphaFold model)
COP9 signalosome complex subunit 4Dprotein406Homo sapiensQ9BT78 (AlphaFold model)
COP9 signalosome complex subunit 5Eprotein334Homo sapiensQ92905
COP9 signalosome complex subunit 6Fprotein327Homo sapiensQ7L5N1
COP9 signalosome complex subunit 7bGprotein264Homo sapiensQ9H9Q2
COP9 signalosome complex subunit 8Hprotein209Homo sapiensQ99627
Kelch repeat and BTB domain-containing protein 2I, Mprotein623Homo sapiensQ8IY47
Cullin-3Lprotein768Homo sapiensQ13618
E3 ubiquitin-protein ligase RBX1Rprotein108Homo sapiensP62877
NEDD8Nprotein76Homo sapiensQ15843
Sequence of entity 1 (A), FASTA
>8H38_1 COP9 signalosome complex subunit 1 (chains A)
MRDSSAPSSASSSVTDLYCTPHSSRSDLVLPGTAGDFSLSASLSACTLLYEGAVEPMQID
VDPQEDPQNAPDVNYVVENPSLDLEQYAASYSGLMRIERLQFIADHCPTLRVEALKMALS
FVQRTFNVDMYEEIHRKLSEATRELQNAPDAIPESGVEPPALDTAWVEATRKKALLKLEK
LDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDYCTSAKHVINMCLN
VIKVSVYLQNWSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKCAAGLAELAARKYK
QAAKCLLLASFDHCDFPELLSPSNVAIYGGLCALATFDRQELQRNVISSSSFKLFLELEP
QVRDIIFKFYESKYASCLKMLDEMKDNLLLDMYLAPHVRTLYTQIRNRALIQYFSPYVSA
DMHRMAAAFNTTVAALEDELTQLILEGLISARVDSHSKILYARDVDQRSTTFEKSLLMGK
EFQRRAKAMMLRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM
Sequence of entity 2 (B), FASTA
>8H38_2 COP9 signalosome complex subunit 2 (chains B)
MSDMEDDFMCDDEEDYDLEYSEDSNSEPNVDLENQYYNSKALKEDDPKAALSSFQKVLEL
EGEKGEWGFKALKQMIKINFKLTNFPEMMNRYKQLLTYIRSAVTRNYSEKSINSILDYIS
TSKQMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQ
TDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIREC
GGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK
PYKNDPEILAMTNLVSAYQNNDITEFEKILKTNHSNIMDDPFIREHIEELLRNIRTQVLI
KLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHGRIDQVNQLLELDHQKRGGAR
YTALDKWTNQLNSLNQAVVSKLA
Sequence of entity 3 (C), FASTA
>8H38_3 COP9 signalosome complex subunit 3 (chains C)
MASALEQFVNSVRQLSAQGQMTQLCELINKSGELLAKNLSHLDTVLGALDVQEHSLGVLA
VLFVKFSMPSVPDFETLFSQVQLFISTCNGEHIRYATDTFAGLCHQLTNALVERKQPLRG
IGILKQAIDKMQMNTNQLTSIHADLCQLCLLAKCFKPALPYLDVDMMDICKENGAYDAKH
FLCYYYYGGMIYTGLKNFERALYFYEQAITTPAMAVSHIMLESYKKYILVSLILLGKVQQ
LPKYTSQIVGRFIKPLSNAYHELAQVYSTNNPSELRNLVNKHSETFTRDNNMGLVKQCLS
SLYKKNIQRLTKTFLTLSLQDMASRVQLSGPQEAEKYVLHMIEDGEIFASINQKDGMVSF
HDNPEKYNNPAMLHNIDQEMLKCIELDERLKAMDQEITVNPQFVQKSMGSQEDDSGNKPS
SYS
Sequence of entity 4 (D), FASTA
>8H38_4 COP9 signalosome complex subunit 4 (chains D)
MAAAVRQDLAQLMNSSGSHKDLAGKYRQILEKAIQLSGAEQLEALKAFVEAMVNENVSLV
ISRQLLTDFCTHLPNLPDSTAKEIYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDW
RNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTN
EQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQ
QRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADGSSIL
DRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVH
FETREALPTWDKQIQSLCFQVNNLLEKISQTAPEWTAQAMEAQMAQ
Sequence of entity 5 (E), FASTA
>8H38_5 COP9 signalosome complex subunit 5 (chains E)
MAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISAL
ALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAY
IENAKQVGRLENAIGWYASHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGK
VNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLEL
LWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQLGRGSFMLGLETHDRKSEDKL
AKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
Sequence of entity 6 (F), FASTA
>8H38_6 COP9 signalosome complex subunit 6 (chains F)
MAAAAAAAAATNGTGGSSGMEVDAAVVPSVMACGVTGSVSVALHPLVILNISDHWIRMRS
QEGRPVQVIGALIGKQEGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELE
FLGWYTTGGPPDPSDIHVHKQVCEIIESPLFLKLNPMTKHTDLPVSVFESVIDIINGEAT
MLFAELTYTLATEEAERIGVDHVARMTATGSGENSTVAEHLIAQHSAIKMLHSRVKLILE
YVKASEAGEVPFNHEILREAYALCHCLPVLSTDKFKTDFYDQCNDVGLMAYLGTITKTCN
TMNQFVNKFNVLYDRQGIGRRMRGLFF
Sequence of entity 7 (G), FASTA
>8H38_7 COP9 signalosome complex subunit 7b (chains G)
MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN
AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL
EMRNLRELEDLIIEAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDG
CEAVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAEREC
PPHAEQRQPTKKMSKVKGLVSSRH
Sequence of entity 8 (H), FASTA
>8H38_8 COP9 signalosome complex subunit 8 (chains H)
MPVAVMAESAFSFKKLLDQCENQELEAPGGIATPPVYGQLLALYLLHNDMNNARYLWKRI
PPAIKSANSELGGIWSVGQRIWQRDFPGIYTTINAHQWSETVQPIMEALRDATRRRAFAL
VSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDVSFNKFI
PLSEPAPVPPIPNEQQLARLTDYVAFLEN
Sequence of entity 9 (I, M), FASTA
>8H38_9 Kelch repeat and BTB domain-containing protein 2 (chains I, M)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV
Sequence of entity 10 (L), FASTA
>8H38_10 Cullin-3 (chains L)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA
Sequence of entity 11 (R), FASTA
>8H38_11 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 12 (N), FASTA
>8H38_12 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4

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 Q13098 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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