8H36: KBTBD2-CUL3-Rbx1-p85a dimeric complex

Name: PDB 8H36: Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex. Determined by electron microscopy at 4.6 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 4.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 28,650
Mol. weight: 513.38 kDa
Ligands: ZN
Released: 11 Oct 2023

Explore 8H36 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H36 contains 143 α-helices and 117 β-strands across 8 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: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-26	15
β-strand	33-37	5	4
β-strand	40-44	5	4
α-helix	46-52	7
α-helix	54-60	7
α-helix	65-67	3
β-strand	71-73	3	4
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	174-181	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	5
β-strand	285-289	5	5
β-strand	294-298	5	5
β-strand	306-312	7	6
β-strand	318-325	8	6
β-strand	345-346	2	6
β-strand	351-354	4	6
β-strand	359-362	4	6
α-helix	364-366	3
β-strand	374-378	5	7
β-strand	381-385	5	7
β-strand	399-402	4	7
β-strand	409-412	4	7
α-helix	413-415	3
β-strand	423-427	5	8
β-strand	430-434	5	8
β-strand	439-443	5	8
β-strand	448-451	4	8
α-helix	453-455	3
β-strand	460-467	8	9
β-strand	470-476	7	9
β-strand	499-503	5	9
β-strand	508-513	6	9
β-strand	527-530	4	10
β-strand	533-541	9	10
β-strand	547-555	9	10
β-strand	560-566	7	10
β-strand	580-586	7	5

Chain B: 23 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-26	15
β-strand	33-37	5	17
β-strand	40-44	5	17
α-helix	46-52	7
α-helix	54-60	7
α-helix	65-68	4
β-strand	71-73	3	17
α-helix	79-90	12
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	242-246	5
α-helix	258-260	3
β-strand	266-274	9	18
α-helix	275-276	2
β-strand	284-289	6	18
β-strand	294-298	5	18
β-strand	306	1	19
β-strand	311-312	2	20
β-strand	318-321	4	20
β-strand	324-325	2	19
β-strand	345-346	2	19
β-strand	350-353	4	20
β-strand	360-362	3	20
β-strand	374-378	5	21
β-strand	381-385	5	21
β-strand	399-403	5	21
β-strand	409-411	3	21
α-helix	413-415	3
β-strand	423-427	5	22
β-strand	430-434	5	22
β-strand	439-443	5	22
β-strand	448-451	4	22
α-helix	453-455	3
β-strand	463-467	5	23
β-strand	470-474	5	23
β-strand	498-503	6	23
β-strand	508-514	7	23
β-strand	524-530	7	24
β-strand	533-541	9	24
β-strand	547-555	9	24
β-strand	560-566	7	24
β-strand	580-586	7	18
β-strand	593	1	18

Chain C: 36 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	71-97	27
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	230-247	18
α-helix	257-268	12
α-helix	273-278	6
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	468-494	27
β-strand	502-503	2	1
β-strand	506-509	4	2
α-helix	526-541	16
β-strand	547-549	3	2
β-strand	557-561	5	1
β-strand	591	1	1
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-635	11
β-strand	645-646	2	16
β-strand	659-660	2	16
β-strand	671	1	1
α-helix	685-710	26
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	30
β-strand	30-34	5	31
β-strand	70-72	3	33
β-strand	78-80	3	33
α-helix	81-85	5
α-helix	86-88	3
β-strand	106	1	33

Chain E: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	30-34	5	2
β-strand	70-72	3	3
β-strand	78-80	3	3
α-helix	81-87	7
β-strand	106	1	3

Chain F: 36 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	70-94	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	230-249	20
α-helix	254-256	3
α-helix	257-278	22
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	467-492	26
β-strand	502-503	2	30
β-strand	506-509	4	31
α-helix	526-541	16
β-strand	547-549	3	31
β-strand	557-561	5	30
β-strand	591	1	30
α-helix	599-607	9
α-helix	613-618	6
α-helix	625-635	11
β-strand	645-646	2	32
β-strand	659-660	2	32
β-strand	671	1	30
α-helix	685-710	26
α-helix	722-729	8
α-helix	738-745	8
α-helix	748-750	3

Chain G: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	334	1	11
α-helix	340-347	8
β-strand	355-359	5	11
β-strand	368-374	7	11
β-strand	377-383	7	11
β-strand	384-385	2	12
β-strand	390-391	2	12
α-helix	401-410	10
β-strand	412	1	13
β-strand	423	1	13
α-helix	436-438	3
α-helix	443-507	65
α-helix	522-579	58
α-helix	584-586	3
α-helix	591-597	7
α-helix	617-619	3
β-strand	625	1	14
α-helix	631-637	7
β-strand	645-650	6	14
β-strand	657-663	7	14
β-strand	666-672	7	14
β-strand	673-674	2	15
β-strand	679-680	2	15
β-strand	688	1	15
α-helix	693-701	9
β-strand	716-717	2	14

Chain H: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	334	1	25
α-helix	342-346	5
β-strand	355-359	5	25
β-strand	368-374	7	25
β-strand	377-383	7	25
β-strand	384-385	2	26
β-strand	390-391	2	26
α-helix	401-409	9
β-strand	412	1	27
β-strand	423	1	27
α-helix	436-438	3
α-helix	443-507	65
α-helix	522-580	59
α-helix	585-587	3
α-helix	591-599	9
α-helix	617-619	3
β-strand	625	1	28
α-helix	631-638	8
α-helix	641-642	2
β-strand	645-650	6	28
β-strand	657-663	7	28
β-strand	666-672	7	28
β-strand	673-675	3	29
β-strand	678-680	3	29
β-strand	688	1	29
α-helix	691-700	10
β-strand	716-717	2	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RBX1	D, E	protein	108	Homo sapiens	P62877 (AlphaFold model)
Kelch repeat and BTB domain-containing protein 2	A, B	protein	623	Homo sapiens	Q8IY47 (AlphaFold model)
Phosphatidylinositol 3-kinase regulatory subunit alpha	G, H	protein	724	Homo sapiens	P27986 (AlphaFold model)
Cullin-3	C, F	protein	768	Homo sapiens	Q13618 (AlphaFold model)

Sequence of entity 1 (D, E), FASTA

>8H36_1 E3 ubiquitin-protein ligase RBX1 (chains D, E)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 2 (A, B), FASTA

>8H36_2 Kelch repeat and BTB domain-containing protein 2 (chains A, B)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKDMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV

Sequence of entity 3 (G, H), FASTA

>8H36_3 Phosphatidylinositol 3-kinase regulatory subunit alpha (chains G, H)
MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIGWLNGYN
ETTGERGDFPGTYVEYIGRKKISPPTPKPRPPRPLPVAPGSSKTEADVEQQALTLPDLAE
QFAPPDIAPPLLIKLVEAIEKKGLECSTLYRTQSSSNLAELRQLLDCDTPSVDLEMIDVH
VLADAFKRYLLDLPNPVIPAAVYSEMISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTL
QYLLKHFFKLSQTSSKNLLNARVLSEIFSPMLFRFSAASSDNTENLIKVIEILISTEWNE
RQPAPALPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDA
STKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKL
DVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMK
RTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIID
SRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGN
ENTEDQYSLVEDDEDLPHHDEKTWNVGSSNRNKAENLLRGKRDGTFLVRESSKQGCYACS
VVVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNVTLAYPVYA
QQRR

Sequence of entity 4 (C, F), FASTA

>8H36_4 Cullin-3 (chains C, F)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETILDKAMVLFR
FMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEGMFRDMSIS
NTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAFEIFRRFYL
AKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHILQVSTFQMT
ILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKEIENGHIFT
VNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHN
VLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA

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

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