8H34: KBTBD2-Cul3-Rbx1 hexameric complex

Name: PDB 8H34: Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex. Determined by electron microscopy at 7.99 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 7.99 Å
Organism: Homo sapiens
Chains: 18
Atoms: 65,663
Mol. weight: 1047.8 kDa
Ligands: ZN
Released: 11 Oct 2023

Explore 8H34 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H34 contains 331 α-helices and 275 β-strands across 18 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: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
β-strand	33-37	5	29
β-strand	40-44	5	29
α-helix	46-52	7
α-helix	56-61	6
β-strand	71-73	3	29
α-helix	79-91	13
α-helix	101-111	11
α-helix	114-125	12
α-helix	132-142	11
α-helix	146-163	18
α-helix	167-170	4
α-helix	174-182	9
α-helix	192-203	12
α-helix	210-220	11
α-helix	222-225	4
α-helix	229-236	8
α-helix	237-238	2
α-helix	243-249	7
β-strand	266-275	10	30
β-strand	283-288	6	30
β-strand	295-298	4	30
β-strand	306	1	31
β-strand	309-312	4	32
β-strand	318-321	4	32
β-strand	324-325	2	31
β-strand	345-346	2	31
β-strand	350-353	4	32
β-strand	360-362	3	32
β-strand	374-378	5	33
β-strand	381-385	5	33
β-strand	399-403	5	33
β-strand	408-411	4	33
α-helix	413-415	3
β-strand	423-427	5	34
β-strand	430-434	5	34
β-strand	439-443	5	34
β-strand	448-451	4	34
β-strand	463-467	5	35
β-strand	470-474	5	35
β-strand	499-503	5	35
β-strand	508-511	4	35
β-strand	524	1	36
β-strand	527-530	4	36
β-strand	533-540	8	36
β-strand	548-555	8	36
β-strand	560-567	8	36
α-helix	568	1
β-strand	580-586	7	30
β-strand	592-593	2	30
α-helix	594-595	2

Chain B: 17 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	11-27	17
β-strand	33-37	5	37
β-strand	40-44	5	37
α-helix	46-52	7
α-helix	57-60	4
β-strand	71-73	3	37
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	167-169	3
α-helix	174-182	9
α-helix	192-202	11
α-helix	210-216	7
α-helix	231-235	5
α-helix	238	1
α-helix	245-249	5
β-strand	266-275	10	38
β-strand	283-288	6	38
β-strand	295-297	3	38
α-helix	299-301	3
β-strand	306	1	39
β-strand	309-312	4	40
β-strand	318-321	4	40
β-strand	324-325	2	39
β-strand	345-346	2	39
β-strand	350-353	4	40
β-strand	360-362	3	40
β-strand	374-378	5	41
β-strand	381-385	5	41
β-strand	400-403	4	41
β-strand	408-411	4	41
α-helix	413-415	3
β-strand	423-427	5	42
β-strand	430-434	5	42
β-strand	439-443	5	42
β-strand	448-451	4	42
β-strand	463-467	5	43
β-strand	470-474	5	43
β-strand	498-503	6	43
β-strand	508-514	7	43
β-strand	524	1	44
β-strand	527-530	4	44
β-strand	533-541	9	44
β-strand	547-555	9	44
β-strand	560-566	7	44
β-strand	580-586	7	38
β-strand	593	1	38

Chain C: 33 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	54-66	13
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	233-251	19
α-helix	258-272	15
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	405-420	16
α-helix	425-440	16
α-helix	450-461	12
α-helix	466-494	29
β-strand	502-503	2	26
β-strand	506-509	4	27
α-helix	526-543	18
β-strand	547-549	3	27
β-strand	557-561	5	26
β-strand	591-594	4	26
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-634	10
β-strand	645-646	2	28
β-strand	659-660	2	28
β-strand	671	1	26
α-helix	685-710	26
α-helix	711-713	3
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-750	3

Chains D and Q: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	45
β-strand	30-33	4	46
β-strand	70-72	3	50
β-strand	78-80	3	50
α-helix	81-85	5
α-helix	100-101	2
β-strand	105-106	2	50

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	26
β-strand	30-34	5	27
β-strand	70-72	3	48
β-strand	78-80	3	48
α-helix	81-87	7
β-strand	93	1	49
β-strand	100	1	49
α-helix	101	1
β-strand	105-106	2	48

Chain F: 34 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	55-66	12
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-95	6
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	233-251	19
α-helix	258-272	15
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	405-420	16
α-helix	425-440	16
α-helix	450-461	12
α-helix	467-493	27
β-strand	502-503	2	45
β-strand	506-509	4	46
α-helix	526-543	18
β-strand	549	1	46
β-strand	557-561	5	45
β-strand	591-594	4	45
α-helix	599-607	9
α-helix	615-618	4
α-helix	625-634	10
β-strand	645-646	2	47
β-strand	659-660	2	47
β-strand	671	1	45
α-helix	685-710	26
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-750	3

Chain G: 19 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	13-27	15
β-strand	33-37	5	51
β-strand	40-44	5	51
α-helix	46-52	7
α-helix	56-61	6
β-strand	71-73	3	51
α-helix	79-91	13
α-helix	101-111	11
α-helix	114-125	12
α-helix	132-142	11
α-helix	146-163	18
α-helix	167-170	4
α-helix	174-182	9
α-helix	192-203	12
α-helix	210-220	11
α-helix	222-225	4
α-helix	229-236	8
α-helix	237-238	2
α-helix	243-249	7
β-strand	266-275	10	52
β-strand	283-288	6	52
β-strand	295-298	4	52
β-strand	306	1	53
β-strand	309-312	4	54
β-strand	318-321	4	54
β-strand	324-325	2	53
β-strand	345-346	2	53
β-strand	350-353	4	54
β-strand	360-362	3	54
β-strand	374-378	5	55
β-strand	381-385	5	55
β-strand	399-403	5	55
β-strand	408-411	4	55
α-helix	413-415	3
β-strand	423-427	5	56
β-strand	430-434	5	56
β-strand	439-443	5	56
β-strand	448-451	4	56
β-strand	463-467	5	57
β-strand	470-474	5	57
β-strand	499-503	5	57
β-strand	508-511	4	57
β-strand	527-530	4	58
β-strand	533-540	8	58
β-strand	548-555	8	58
β-strand	560-567	8	58
α-helix	568	1
β-strand	580-586	7	52
β-strand	592-593	2	52
α-helix	594-595	2

Chain H: 34 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	54-66	13
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-95	6
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	233-251	19
α-helix	258-277	20
α-helix	285-289	5
α-helix	294-303	10
α-helix	309-329	21
α-helix	339-358	20
α-helix	364-380	17
α-helix	384-397	14
α-helix	406-420	15
α-helix	425-436	12
α-helix	437-441	5
α-helix	450-459	10
α-helix	467-493	27
β-strand	502-503	2	70
β-strand	506-509	4	71
α-helix	526-541	16
β-strand	547-549	3	71
β-strand	557-561	5	70
β-strand	591-594	4	70
α-helix	599-607	9
α-helix	615-618	4
α-helix	625-634	10
β-strand	645-646	2	72
β-strand	659-660	2	72
β-strand	671	1	70
α-helix	685-711	27
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-750	3

8 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
Cullin-3	C, F, H, I, M, O	protein	768	Homo sapiens	Q13618 (AlphaFold model)
Kelch repeat and BTB domain-containing protein 2	A, B, G, J, N, P	protein	623	Homo sapiens	Q8IY47 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	D, E, K, L, Q, R	protein	121	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (C, F, H, I, M, O), FASTA

>8H34_1 Cullin-3 (chains C, F, H, I, M, O)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA

Sequence of entity 2 (A, B, G, J, N, P), FASTA

>8H34_2 Kelch repeat and BTB domain-containing protein 2 (chains A, B, G, J, N, P)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

Sequence of entity 3 (D, E, K, L, Q, R), FASTA

>8H34_3 E3 ubiquitin-protein ligase RBX1 (chains D, E, K, L, Q, R)
HHHHHHENLYFQGMAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRN
HIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG
H

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	18

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 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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