8H33: KBTBD2-Cul3-Rbx1 tetrameric complex

Name: PDB 8H33: Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex. Determined by electron microscopy at 7.86 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 7.86 Å
Organism: Homo sapiens
Chains: 12
Atoms: 43,548
Mol. weight: 702.7 kDa
Ligands: ZN
Released: 11 Oct 2023

Explore 8H33 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H33 contains 201 α-helices and 199 β-strands across 12 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	33-37	5	1
β-strand	40-44	5	1
α-helix	46-52	7
α-helix	56-61	6
α-helix	65-68	4
β-strand	71-73	3	1
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	192-201	10
α-helix	212-219	8
α-helix	227-236	10
α-helix	238	1
α-helix	243-250	8
β-strand	266-272	7	2
β-strand	274-275	2	3
β-strand	283-284	2	3
β-strand	285-288	4	2
β-strand	295-298	4	2
β-strand	306	1	4
β-strand	309-312	4	5
β-strand	318-321	4	5
β-strand	324-325	2	4
β-strand	345-346	2	4
β-strand	350-353	4	5
β-strand	360-362	3	5
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	399-403	5	6
β-strand	408-411	4	6
α-helix	413-415	3
β-strand	423-426	4	7
β-strand	431-434	4	7
β-strand	439-443	5	7
β-strand	448-451	4	7
β-strand	463-467	5	8
β-strand	470-474	5	8
β-strand	499-503	5	8
β-strand	508-511	4	8
β-strand	524	1	9
β-strand	527-530	4	9
β-strand	533-540	8	9
β-strand	548-555	8	9
β-strand	560-567	8	9
β-strand	580-586	7	2
β-strand	592-593	2	2

Chain B: 17 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	14-26	13
β-strand	33-37	5	10
β-strand	40-44	5	10
α-helix	46-52	7
α-helix	56-61	6
β-strand	71-73	3	10
α-helix	79-91	13
α-helix	101-110	10
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	192-200	9
α-helix	207-209	3
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	527-529	3	18
β-strand	534-540	7	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 C: 33 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	49-51	3
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	201	1
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	364-377	14
α-helix	384-397	14
α-helix	405-421	17
α-helix	425-440	16
α-helix	450-458	9
α-helix	468-493	26
β-strand	502-503	2	54
β-strand	506-509	4	55
α-helix	526-542	17
β-strand	548-549	2	55
β-strand	557-561	5	54
β-strand	591	1	54
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-634	10
β-strand	645-646	2	56
β-strand	659-660	2	56
β-strand	671	1	54
α-helix	685-711	27
α-helix	722-727	6
α-helix	738-745	8
α-helix	747-750	4

Chains D and L: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	37
β-strand	30-33	4	38
β-strand	70-72	3	39
β-strand	78-80	3	39
α-helix	81-87	7
β-strand	93	1	40
β-strand	100	1	40
α-helix	101	1
β-strand	105-106	2	39

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	54
β-strand	30-33	4	55
β-strand	70-72	3	57
β-strand	78-80	3	57
α-helix	81-90	10
β-strand	93	1	58
β-strand	100	1	58
α-helix	101	1
β-strand	105-106	2	57

Chain F: 28 helices, 10 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	200-227	28
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	338-358	21
α-helix	364-380	17
α-helix	383-398	16
α-helix	405-421	17
α-helix	425-440	16
α-helix	450-461	12
α-helix	464-491	28
β-strand	502-503	2	37
β-strand	506-509	4	38
α-helix	527-541	15
β-strand	544	1	41
β-strand	546	1	41
β-strand	549	1	38
β-strand	557-561	5	37
β-strand	591	1	37
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-634	10
β-strand	645-646	2	42
β-strand	659-660	2	42
β-strand	671	1	37
α-helix	685-711	27
α-helix	722-729	8
α-helix	738-745	8

Chain G: 18 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	14-26	13
β-strand	33-37	5	19
β-strand	40-44	5	19
α-helix	46-49	4
α-helix	54-61	8
α-helix	65-68	4
β-strand	71-73	3	19
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	192-204	13
α-helix	211-219	9
α-helix	221-226	6
α-helix	229-236	8
α-helix	238	1
α-helix	243-250	8
β-strand	266-271	6	20
β-strand	274	1	21
β-strand	284	1	21
β-strand	285-288	4	20
β-strand	295-298	4	20
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	350-353	4	23
β-strand	360-362	3	23
β-strand	374-378	5	24
β-strand	381-385	5	24
β-strand	399-403	5	24
β-strand	408-410	3	24
α-helix	413-415	3
β-strand	423-426	4	25
β-strand	431-434	4	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	533-540	8	27
β-strand	548-555	8	27
β-strand	560-567	8	27
β-strand	581-586	6	20
β-strand	592-593	2	20

Chain H: 33 helices, 7 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	233-250	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	364-377	14
α-helix	383-398	16
α-helix	405-420	16
α-helix	425-440	16
α-helix	450-461	12
α-helix	466-494	29
α-helix	498-500	3
β-strand	506-509	4	43
α-helix	526-541	16
β-strand	547-549	3	43
β-strand	557-561	5	44
β-strand	591	1	44
α-helix	599-607	9
α-helix	613-618	6
α-helix	628-634	7
β-strand	645-646	2	45
β-strand	659-660	2	45
β-strand	671	1	44
α-helix	685-710	26
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-751	4

3 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
Kelch repeat and BTB domain-containing protein 2	A, B, G, J	protein	623	Homo sapiens	Q8IY47 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	D, E, K, L	protein	121	Homo sapiens	P62877 (AlphaFold model)
Cullin-3	C, F, H, I	protein	776	Homo sapiens	Q13618 (AlphaFold model)

Sequence of entity 1 (A, B, G, J), FASTA

>8H33_1 Kelch repeat and BTB domain-containing protein 2 (chains A, B, G, J)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

Sequence of entity 2 (D, E, K, L), FASTA

>8H33_2 E3 ubiquitin-protein ligase RBX1 (chains D, E, K, L)
HHHHHHENLYFQGMAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRN
HIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG
H

Sequence of entity 3 (C, F, H, I), FASTA

>8H33_3 Cullin-3 (chains C, F, H, I)
WSHPQFEKMSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGL
SFEELYRNAYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDH
QTAMVMIRDILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARE
RKGEVVDRGAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASV
YIKKVEARINEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGK
TEDLGCMYKLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRF
DRFLLESFNNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETIL
DKAMVLFRFMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEG
MFRDMSISNTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAF
EIFRRFYLAKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHIL
QVSTFQMTILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKE
IENGHIFTVNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMK
SRKKMQHNVLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

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 Q8IY47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GQ6 3.96 Å, Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex
8H38 4.25 Å, Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex
8H36 4.6 Å, Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex
8H3R 6.36 Å, Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex
8H3F 6.73 Å, Cryo-EM Structure of the KBTBD2-CRL3-CSN complex
8H35 7.41 Å, Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex
8H3A 7.51 Å, Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex
8H37 7.52 Å, Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex
8H34 7.99 Å, Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex

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