8H35: KBTBD2-Cul3-Rbx1 octameric complex

Name: PDB 8H35: Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex. Determined by electron microscopy at 7.41 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 7.41 Å
Organism: Homo sapiens
Chains: 24
Atoms: 86,872
Mol. weight: 1383.62 kDa
Ligands: ZN
Released: 11 Oct 2023

Explore 8H35 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H35 contains 448 α-helices and 371 β-strands across 24 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	13-27	15
β-strand	34-37	4	7
β-strand	40-42	3	7
α-helix	46-52	7
α-helix	56-61	6
β-strand	71-73	3	7
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	8
β-strand	283-288	6	8
β-strand	295-298	4	8
β-strand	306	1	9
β-strand	309-312	4	10
β-strand	318-321	4	10
β-strand	324-325	2	9
β-strand	345-346	2	9
β-strand	350-353	4	10
β-strand	360-362	3	10
β-strand	374-378	5	11
β-strand	381-385	5	11
β-strand	399-403	5	11
β-strand	408-411	4	11
α-helix	413-415	3
β-strand	423-427	5	12
β-strand	430-434	5	12
β-strand	439-442	4	12
β-strand	449-451	3	12
β-strand	463-467	5	13
β-strand	470-474	5	13
β-strand	499-503	5	13
β-strand	508-511	4	13
β-strand	524	1	14
β-strand	527-530	4	14
β-strand	533-540	8	14
β-strand	548-555	8	14
β-strand	560-567	8	14
α-helix	568	1
β-strand	580-586	7	8
β-strand	592-593	2	8
α-helix	594-595	2

Chain B: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	11-27	17
β-strand	33-37	5	15
β-strand	40-44	5	15
α-helix	46-52	7
α-helix	57-60	4
α-helix	65-68	4
β-strand	71-73	3	15
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	16
α-helix	276	1
β-strand	283-288	6	16
β-strand	295-298	4	16
α-helix	299-301	3
β-strand	306	1	17
β-strand	309-312	4	18
β-strand	318-321	4	18
β-strand	324-325	2	17
β-strand	345-346	2	17
β-strand	350-353	4	18
β-strand	360-362	3	18
β-strand	374-378	5	19
β-strand	381-385	5	19
β-strand	400-403	4	19
β-strand	408-411	4	19
α-helix	413-415	3
β-strand	423-427	5	20
β-strand	430-434	5	20
β-strand	439-443	5	20
β-strand	448-451	4	20
β-strand	463-467	5	21
β-strand	470-474	5	21
β-strand	498-503	6	21
β-strand	508-514	7	21
β-strand	524	1	22
β-strand	527-530	4	22
β-strand	533-541	9	22
β-strand	547-555	9	22
β-strand	560-566	7	22
β-strand	580-586	7	16
β-strand	593	1	16

Chain C: 34 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	450-458	9
α-helix	459-463	5
α-helix	464-493	30
β-strand	502-503	2	1
β-strand	506-509	4	2
α-helix	526-542	17
β-strand	546-549	4	2
β-strand	557-561	5	1
β-strand	591-594	4	1
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-634	10
β-strand	645-646	2	3
β-strand	659-660	2	3
β-strand	671	1	1
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	4
β-strand	30-34	5	5
β-strand	70-72	3	25
β-strand	78-80	3	25
α-helix	81-85	5
α-helix	100-101	2
β-strand	105-106	2	25

Chains E, L and W: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	30-35	6	2
β-strand	70-72	3	23
β-strand	78-80	3	23
α-helix	81-87	7
β-strand	93	1	24
β-strand	100	1	24
α-helix	101	1
β-strand	105-106	2	23

Chain F: 34 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	54-64	11
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	309-329	21
α-helix	338-358	21
α-helix	364-379	16
α-helix	384-397	14
α-helix	405-420	16
α-helix	425-440	16
α-helix	450-461	12
α-helix	467-494	28
β-strand	502-503	2	4
β-strand	506-509	4	5
α-helix	526-541	16
β-strand	547-549	3	5
β-strand	557-561	5	4
β-strand	591-594	4	4
α-helix	599-607	9
α-helix	615-618	4
α-helix	625-634	10
β-strand	645-646	2	6
β-strand	659-660	2	6
β-strand	671	1	4
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

Chain G: 20 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	15-27	13
β-strand	33-37	5	26
β-strand	40-44	5	26
α-helix	46-52	7
α-helix	56-61	6
β-strand	71-73	3	26
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	27
β-strand	283-288	6	27
β-strand	295-298	4	27
β-strand	306	1	28
β-strand	309-312	4	29
β-strand	318-321	4	29
β-strand	324-325	2	28
β-strand	345-346	2	28
β-strand	350-353	4	29
β-strand	360-362	3	29
β-strand	374-378	5	30
β-strand	381-385	5	30
β-strand	399-403	5	30
β-strand	408-411	4	30
α-helix	413-415	3
β-strand	423-427	5	31
β-strand	430-434	5	31
β-strand	439-443	5	31
β-strand	448-451	4	31
β-strand	463-467	5	32
β-strand	470-474	5	32
β-strand	499-503	5	32
β-strand	508-511	4	32
β-strand	527-530	4	33
β-strand	533-540	8	33
β-strand	548-555	8	33
β-strand	560-567	8	33
α-helix	568	1
β-strand	580-586	7	27
β-strand	592-593	2	27
α-helix	594-595	2

Chain H: 36 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	467-494	28
β-strand	502-503	2	46
β-strand	506-509	4	47
α-helix	523-525	3
α-helix	526-538	13
β-strand	549	1	47
β-strand	557-561	5	46
β-strand	591-594	4	46
α-helix	599-607	9
α-helix	615-618	4
α-helix	625-634	10
β-strand	645-646	2	48
β-strand	659-660	2	48
β-strand	671	1	46
α-helix	685-709	25
α-helix	711-713	3
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-750	3

12 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, T, V	protein	768	Homo sapiens	Q13618 (AlphaFold model)
Kelch repeat and BTB domain-containing protein 2	A, B, G, J, N, P, S, U	protein	623	Homo sapiens	Q8IY47 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	D, E, K, L, Q, R, W, X	protein	108	Homo sapiens	P62877 (AlphaFold model)

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

>8H35_1 Cullin-3 (chains C, F, H, I, M, O, T, V)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA

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

>8H35_2 Kelch repeat and BTB domain-containing protein 2 (chains A, B, G, J, N, P, S, U)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

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

>8H35_3 E3 ubiquitin-protein ligase RBX1 (chains D, E, K, L, Q, R, W, X)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	24

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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