8H3R: KBTBD2-CRL3~N8 dimeric complex

Name: PDB 8H3R: Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex. Determined by electron microscopy at 6.36 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 6.36 Å
Organism: Homo sapiens
Chains: 6
Atoms: 22,313
Mol. weight: 345.91 kDa
Ligands: ZN
Released: 11 Oct 2023

Explore 8H3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H3R contains 106 α-helices and 96 β-strands across 6 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: 17 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	14-26	13
β-strand	34-37	4	10
β-strand	40-42	3	10
α-helix	46-52	7
α-helix	54-59	6
α-helix	65-68	4
β-strand	71-73	3	10
α-helix	79-91	13
α-helix	101-111	11
α-helix	114-126	13
α-helix	133-142	10
α-helix	146-163	18
α-helix	167-170	4
α-helix	174-182	9
α-helix	192-205	14
α-helix	210-225	16
α-helix	229-236	8
α-helix	238	1
α-helix	243-250	8
β-strand	266-272	7	11
β-strand	274-275	2	12
β-strand	283-284	2	12
β-strand	285-288	4	11
β-strand	295-298	4	11
β-strand	306	1	13
β-strand	309-312	4	14
β-strand	318-321	4	14
β-strand	324-325	2	13
β-strand	345-346	2	13
β-strand	350-353	4	14
β-strand	360-362	3	14
β-strand	374-378	5	15
β-strand	381-385	5	15
β-strand	399-403	5	15
β-strand	408-411	4	15
α-helix	413-415	3
β-strand	423-426	4	16
β-strand	431-434	4	16
β-strand	439-443	5	16
β-strand	448-451	4	16
β-strand	463-467	5	17
β-strand	470-474	5	17
β-strand	499-503	5	17
β-strand	508-511	4	17
β-strand	524	1	18
β-strand	527-530	4	18
β-strand	533-540	8	18
β-strand	548-555	8	18
β-strand	560-567	8	18
β-strand	580-586	7	11
β-strand	592-593	2	11

Chain B: 19 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	11-26	16
β-strand	34-37	4	19
β-strand	40-43	4	19
α-helix	46-52	7
α-helix	54-60	7
α-helix	65-67	3
β-strand	71-72	2	19
α-helix	79-91	13
α-helix	101-111	11
α-helix	114-127	14
α-helix	133-142	10
α-helix	146-163	18
α-helix	174-181	8
α-helix	193-203	11
α-helix	210-216	7
α-helix	222-224	3
α-helix	231-235	5
α-helix	238	1
α-helix	245-249	5
β-strand	266-272	7	20
β-strand	274-275	2	21
α-helix	276	1
β-strand	283-284	2	21
β-strand	285-288	4	20
β-strand	295-298	4	20
α-helix	299-301	3
β-strand	306	1	22
β-strand	309-312	4	23
β-strand	318-321	4	23
β-strand	324-325	2	22
β-strand	345-346	2	22
β-strand	351-354	4	23
β-strand	359-362	4	23
β-strand	374-378	5	24
β-strand	381-385	5	24
β-strand	400-403	4	24
β-strand	408-411	4	24
α-helix	413-415	3
β-strand	423-427	5	25
β-strand	430-434	5	25
β-strand	439-443	5	25
β-strand	448-451	4	25
β-strand	463-467	5	26
β-strand	470-474	5	26
β-strand	499-503	5	26
β-strand	508-511	4	26
β-strand	524	1	27
β-strand	527-530	4	27
β-strand	533-541	9	27
β-strand	547-555	9	27
β-strand	560-565	6	27
β-strand	580-586	7	20
β-strand	593	1	20

Chain C: 31 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	55-66	12
α-helix	70-95	26
α-helix	101-133	33
α-helix	139-147	9
α-helix	148-152	5
α-helix	157-174	18
α-helix	181-194	14
α-helix	200-201	2
α-helix	202-206	5
α-helix	207-227	21
α-helix	233-250	18
α-helix	258-275	18
α-helix	285-289	5
α-helix	293-303	11
α-helix	309-328	20
α-helix	338-355	18
α-helix	356-360	5
α-helix	364-378	15
α-helix	384-397	14
α-helix	406-420	15
α-helix	425-439	15
α-helix	449-459	11
α-helix	467-494	28
β-strand	502-503	2	1
β-strand	506-509	4	2
α-helix	526-541	16
β-strand	546	1	3
β-strand	549	1	2
β-strand	557-561	5	1
β-strand	591	1	1
α-helix	598-607	10
α-helix	613-616	4
α-helix	626-632	7
β-strand	644-646	3	9
β-strand	659-661	3	9
α-helix	685-713	29
α-helix	723-729	7
α-helix	740-748	9

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	5
β-strand	30-33	4	6
β-strand	35	1	7
α-helix	54-57	4
β-strand	70-72	3	8
β-strand	78-80	3	8
α-helix	81-85	5
α-helix	86-88	3
β-strand	105-106	2	8

Chain E: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	30-33	4	2
β-strand	35	1	3
α-helix	54-56	3
β-strand	70-72	3	4
β-strand	78-80	3	4
α-helix	81-90	10
β-strand	105-106	2	4

Chain F: 34 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-43	17
α-helix	44-48	5
α-helix	49-51	3
α-helix	55-58	4
α-helix	62-66	5
α-helix	70-95	26
α-helix	101-133	33
α-helix	139-147	9
α-helix	148-152	5
α-helix	157-174	18
α-helix	181-194	14
α-helix	200-201	2
α-helix	202-206	5
α-helix	207-227	21
α-helix	233-250	18
α-helix	258-275	18
α-helix	285-289	5
α-helix	293-303	11
α-helix	309-328	20
α-helix	338-355	18
α-helix	356-360	5
α-helix	364-378	15
α-helix	384-397	14
α-helix	406-420	15
α-helix	425-441	17
α-helix	450-460	11
α-helix	467-492	26
β-strand	502-503	2	5
β-strand	506-509	4	6
α-helix	526-541	16
β-strand	546	1	7
β-strand	549	1	6
β-strand	557-561	5	5
β-strand	591	1	5
α-helix	598-607	10
α-helix	613-618	6
α-helix	626-632	7
β-strand	644-646	3	28
β-strand	659-661	3	28
α-helix	685-711	27
α-helix	723-729	7
α-helix	740-749	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RBX1	D, E	protein	108	Homo sapiens	P62877 (AlphaFold model)
Cullin-3	C, F	protein	768	Homo sapiens	Q13618 (AlphaFold model)
Kelch repeat and BTB domain-containing protein 2	A, B	protein	623	Homo sapiens	Q8IY47 (AlphaFold model)

Sequence of entity 1 (D, E), FASTA

>8H3R_1 E3 ubiquitin-protein ligase RBX1 (chains D, E)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 2 (C, F), FASTA

>8H3R_2 Cullin-3 (chains C, F)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA

Sequence of entity 3 (A, B), FASTA

>8H3R_3 Kelch repeat and BTB domain-containing protein 2 (chains A, B)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

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 P62877 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DPL 2.6 Å, Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control…
7Z8R 2.7 Å, CAND1-CUL1-RBX1
7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
7PLO 2.8 Å, H. sapiens replisome-CUL2/LRR1 complex
7Z8B 2.8 Å, Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING…
8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
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
1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
3DQV 3.0 Å, Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control…
4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked

Browse structure collections

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