8K9I: CUL3-RBX1-KLHL22 complex without CUL3 NA motif

Name: PDB 8K9I: Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif
Published: 2024-05-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif. Determined by electron microscopy at 4.2 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,657
Mol. weight: 140.45 kDa
Released: 29 May 2024

Explore 8K9I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K9I contains 49 α-helices and 22 β-strands across 4 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 C: 37 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	54-66	13
α-helix	70-85	16
α-helix	86-90	5
α-helix	91-94	4
α-helix	101-120	20
α-helix	124-126	3
α-helix	127-131	5
α-helix	132-133	2
α-helix	139-150	12
α-helix	157-174	18
α-helix	180-194	15
α-helix	199-201	3
α-helix	202-206	5
α-helix	207-224	18
α-helix	230-251	22
α-helix	257-268	12
α-helix	270-272	3
α-helix	276-278	3
α-helix	284-289	6
α-helix	293-304	12
α-helix	309-329	21
α-helix	338-358	21
α-helix	364-380	17
α-helix	384-388	5
α-helix	392-396	5
α-helix	405-421	17
α-helix	425-441	17
α-helix	448-460	13
α-helix	464-494	31
β-strand	508	1	1
α-helix	526-542	17
β-strand	546	1	2
β-strand	549-550	2	1
β-strand	558-559	2	3
β-strand	591-593	3	3
α-helix	596-607	12
β-strand	610-612	3	4
α-helix	613-620	8
α-helix	630-635	6
β-strand	645	1	4
β-strand	658-660	3	4
β-strand	671-673	3	3
α-helix	685-713	29
β-strand	716-717	2	5
α-helix	719-730	12
α-helix	738-750	13
β-strand	756	1	5
β-strand	764-765	2	5

Chain K: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	32-42	11
β-strand	52-54	3	6
β-strand	61-63	3	6
α-helix	65-68	4
α-helix	74-79	6
α-helix	98-108	11
β-strand	116	1	7
β-strand	119	1	7
α-helix	121-129	9
α-helix	133-145	13

Chain L: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	36-45	10
β-strand	52-54	3	8
β-strand	55	1	9
β-strand	61-63	3	8
α-helix	65-71	7
β-strand	92	1	9
α-helix	103-109	7
α-helix	122-129	8
α-helix	133-141	9

Chain R: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	1
β-strand	35	1	2
α-helix	54-57	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-3	C	protein	752	Homo sapiens	Q13618 (AlphaFold model)
Kelch-like protein 22	K, L	protein	178	Homo sapiens	Q53GT1 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R	protein	108	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>8K9I_1 Cullin-3 (chains C)
MDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRNAYTMVLHKHGEKLYTGLREVVTEH
LINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIRDILMYMDRVYVQQNNVENVYNLGL
IIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDRGAIRNACQMLMILGLEGRSVYEED
FEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEARINEEIERVMHCLDKSTEEPIVKVV
ERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMYKLFSRVPNGLKTMCECMSSYLREQ
GKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESFNNDRLFKQTIAGDFEYFLNLNSRS
PEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFRFMQEKDVFERYYKQHLARRLLTNK
SVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSISNTTMDEFRQHLQATGVSLGGVDLT
VRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYLAKHSGRQLTLQHHMGSADLNATFY
GPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMTILMLFNNREKYTFEEIQQETDIPE
RELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFTVNDQFTSKLHRVKIQTVAAKQGES
DPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPSPVVIKKR
IEGLIEREYLARTPEDRKVYTYVAKLHHHHHH

Sequence of entity 2 (K, L), FASTA

>8K9I_2 Kelch-like protein 22 (chains K, L)
MAEEQEFTQLCKLPAQPSHPHCVNNTYRSAQHSQALLRGLLALRDSGILFDVVLVVEGRH
IEAHRILLAASCDYFRGMFAGGLKEMEQEEVLIHGVSYNAMCQILHFIYTSELELSLSNV
QETLVAACQLQIPEIIHFCCDFLMSWVDEENILDVYRLAELFDLSRLTEQLDTYILKN

Sequence of entity 3 (R), FASTA

>8K9I_3 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Primary citation

A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3 KLHL22. Wang, W., Liang, L., Dai, Z. et al. Nat Commun (2024) 15:3789-3789. DOI 10.1038/s41467-024-48045-2 · PubMed

Other PDB entries of the same protein (UniProt Q13618 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6I2M 2.3 Å, Crystal structure of vaccinia virus protein A55 BTB-Back domain in complex with human…
4EOZ 2.4 Å, Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain
4AP2 2.8 Å, Crystal structure of the human KLHL11-Cul3 complex at 2.8A resolution
8I79 2.8 Å, Cryo-EM structure of KCTD7 in complex with Cullin3
4APF 3.1 Å, Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution
9RWZ 3.1 Å, ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO
9Q3E 3.3 Å, Cryo-EM structure of RotavirusA NSP1-ELOB-ELOC-CUL3
5NLB 3.45 Å, Crystal structure of human CUL3 N-terminal domain bound to KEAP1 BTB and 3-box
4HXI 3.51 Å, Crystal structure of KLHL3/Cul3 complex
8U80 3.6 Å, KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD)
8KHP 3.67 Å, CULLIN3-KLHL22-RBX1 E3 ligase
8H3Q 3.76 Å, Cryo-EM Structure of the CAND1-Cul3-Rbx1 complex

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