8H37: KBTBD2-CUL3-Rbx1-p85a tetrameric complex

Name: PDB 8H37: Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex. Determined by electron microscopy at 7.52 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 7.52 Å
Organism: Homo sapiens
Chains: 16
Atoms: 49,321
Mol. weight: 1026.76 kDa
Ligands: ZN
Released: 11 Oct 2023

Explore 8H37 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H37 contains 258 α-helices and 176 β-strands across 16 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: 21 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	12-26	15
β-strand	33-37	5	17
β-strand	40-44	5	17
α-helix	46-50	5
α-helix	54-60	7
α-helix	65-67	3
β-strand	71-73	3	17
α-helix	79-90	12
β-strand	92	1	18
α-helix	101-111	11
α-helix	114-125	12
α-helix	133-143	11
α-helix	146-158	13
α-helix	160-163	4
α-helix	167-170	4
α-helix	174-181	8
α-helix	191-204	14
α-helix	206-209	4
α-helix	210-212	3
α-helix	213-217	5
α-helix	229-233	5
α-helix	242-249	8
α-helix	258-260	3
α-helix	261-263	3
β-strand	266-272	7	19
β-strand	274	1	20
β-strand	284	1	20
β-strand	288	1	19
β-strand	295	1	19
β-strand	306	1	21
β-strand	319-320	2	22
β-strand	324-325	2	21
β-strand	345-346	2	21
β-strand	350-353	4	22
β-strand	360-363	4	22
β-strand	377-378	2	23
β-strand	381-382	2	23
β-strand	383	1	24
β-strand	400	1	25
β-strand	401	1	24
β-strand	411	1	25
β-strand	422	1	26
β-strand	426	1	27
β-strand	431	1	27
β-strand	440	1	28
β-strand	451	1	28
β-strand	462	1	26
β-strand	463	1	29
β-strand	471-472	2	30
β-strand	474	1	29
β-strand	500-502	3	30
β-strand	509-511	3	30
β-strand	527-528	2	31
β-strand	535-539	5	31
β-strand	549-554	6	31
α-helix	555	1
β-strand	561-563	3	31
β-strand	580-586	7	19

Chain B: 21 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	18
α-helix	11-26	16
β-strand	33-37	5	32
β-strand	40-44	5	32
α-helix	46-52	7
α-helix	54-62	9
α-helix	65-68	4
β-strand	71-73	3	32
α-helix	79-91	13
α-helix	101-111	11
α-helix	114-125	12
α-helix	133-143	11
α-helix	146-158	13
α-helix	160-163	4
α-helix	167-170	4
α-helix	174-182	9
α-helix	191-202	12
α-helix	206-209	4
α-helix	210-212	3
α-helix	213-217	5
α-helix	230-233	4
α-helix	242-249	8
α-helix	258-260	3
β-strand	266-274	9	33
β-strand	284-289	6	33
β-strand	294-298	5	33
β-strand	306	1	34
β-strand	311-312	2	35
β-strand	318-321	4	35
β-strand	324-325	2	34
β-strand	345-346	2	34
β-strand	350-353	4	35
β-strand	360-362	3	35
β-strand	374-378	5	36
β-strand	381-385	5	36
β-strand	399-403	5	36
β-strand	408-411	4	36
α-helix	413-415	3
β-strand	423-427	5	37
β-strand	430-434	5	37
β-strand	439-443	5	37
β-strand	448-451	4	37
α-helix	453-455	3
β-strand	463-467	5	38
β-strand	470-474	5	38
β-strand	498-503	6	38
β-strand	508-514	7	38
β-strand	524-530	7	39
β-strand	533-541	9	39
β-strand	547-555	9	39
β-strand	560-566	7	39
β-strand	580-586	7	33

Chain C: 40 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	49-51	3
α-helix	54-66	13
α-helix	70-88	19
α-helix	90-95	6
α-helix	101-122	22
α-helix	124-129	6
α-helix	136-138	3
α-helix	139-146	8
α-helix	147-152	6
α-helix	155-173	19
α-helix	180-192	13
α-helix	199-201	3
α-helix	202-206	5
α-helix	207-225	19
α-helix	230-250	21
α-helix	254-256	3
α-helix	259-264	6
α-helix	265-270	6
α-helix	271-277	7
α-helix	284-290	7
α-helix	293-303	11
α-helix	309-328	20
α-helix	339-355	17
α-helix	356-360	5
α-helix	364-377	14
α-helix	384-397	14
α-helix	406-420	15
α-helix	425-440	16
α-helix	450-461	12
α-helix	467-493	27
β-strand	506-509	4	1
α-helix	526-542	17
β-strand	549	1	1
β-strand	557-561	5	2
β-strand	591	1	2
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-635	11
β-strand	645-646	2	3
β-strand	659-660	2	3
β-strand	671	1	2
α-helix	685-702	18
α-helix	705-710	6
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-750	3

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	4
β-strand	30-33	4	5
β-strand	70-72	3	14
β-strand	78-80	3	14
α-helix	81-85	5
α-helix	86-88	3
β-strand	106	1	14

Chain E: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	2
β-strand	30-33	4	1
β-strand	70-72	3	13
β-strand	78-80	3	13
α-helix	81-90	10
β-strand	106	1	13

Chain F: 35 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	55-66	12
α-helix	70-94	25
α-helix	101-122	22
α-helix	124-129	6
α-helix	136-138	3
α-helix	139-146	8
α-helix	147-152	6
α-helix	155-173	19
α-helix	180-192	13
α-helix	199-201	3
α-helix	202-206	5
α-helix	207-225	19
α-helix	230-250	21
α-helix	257-267	11
α-helix	271-279	9
α-helix	284-290	7
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	406-420	15
α-helix	425-440	16
α-helix	450-461	12
α-helix	467-493	27
β-strand	502-503	2	4
β-strand	506-509	4	5
α-helix	522-525	4
α-helix	526-542	17
β-strand	557-561	5	4
β-strand	591	1	4
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-635	11
β-strand	645-646	2	6
β-strand	659-660	2	6
β-strand	671	1	4
α-helix	685-710	26
α-helix	722-729	8
α-helix	738-745	8

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	436-438	3
α-helix	443-507	65
α-helix	522-583	62
α-helix	584-586	3
α-helix	591-599	9

Chain H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	443-507	65
α-helix	522-582	61
α-helix	585-588	4
α-helix	591-599	9

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, M, O	protein	768	Homo sapiens	Q13618 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	D, E, Q, R	protein	108	Homo sapiens	P62877 (AlphaFold model)
Kelch repeat and BTB domain-containing protein 2	A, B, N, P	protein	623	Homo sapiens	Q8IY47 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	G, H, I, J	protein	724	Homo sapiens	P27986 (AlphaFold model)

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

>8H37_1 Cullin-3 (chains C, F, M, O)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA

Sequence of entity 2 (D, E, Q, R), FASTA

>8H37_2 E3 ubiquitin-protein ligase RBX1 (chains D, E, Q, R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 3 (A, B, N, P), FASTA

>8H37_3 Kelch repeat and BTB domain-containing protein 2 (chains A, B, N, P)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKDMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

Sequence of entity 4 (G, H, I, J), FASTA

>8H37_4 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains G, H, I, J)
MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIGWLNGYN
ETTGERGDFPGTYVEYIGRKKISPPTPKPRPPRPLPVAPGSSKTEADVEQQALTLPDLAE
QFAPPDIAPPLLIKLVEAIEKKGLECSTLYRTQSSSNLAELRQLLDCDTPSVDLEMIDVH
VLADAFKRYLLDLPNPVIPAAVYSEMISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTL
QYLLKHFFKLSQTSSKNLLNARVLSEIFSPMLFRFSAASSDNTENLIKVIEILISTEWNE
RQPAPALPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDA
STKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKL
DVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMK
RTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIID
SRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGN
ENTEDQYSLVEDDEDLPHHDEKTWNVGSSNRNKAENLLRGKRDGTFLVRESSKQGCYACS
VVVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNVTLAYPVYA
QQRR

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 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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