9DTG: Apo KBTBD4

The cryo-EM structure of apo KBTBD4. Determined by electron microscopy at 3.83 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 3.83 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,069
Mol. weight: 119.94 kDa
Released: 27 Nov 2024

Explore 9DTG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DTG contains 44 α-helices and 90 β-strands across 2 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: 22 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
β-strand	18	1	1
β-strand	21-22	2	2
α-helix	36-40	5
β-strand	47	1	3
β-strand	48-51	4	4
β-strand	58	1	3
α-helix	62-66	5
α-helix	68-75	8
α-helix	79-82	4
β-strand	85-88	4	4
α-helix	93-104	12
β-strand	107	1	5
α-helix	113-115	3
α-helix	117-124	8
α-helix	131-138	8
α-helix	150-154	5
α-helix	160-163	4
α-helix	174-177	4
α-helix	181-184	4
α-helix	188-194	7
α-helix	195-197	3
β-strand	199-200	2	6
α-helix	201-203	3
α-helix	205-212	8
α-helix	222-229	8
β-strand	233-234	2	6
α-helix	235-238	4
β-strand	240	1	7
β-strand	243-244	2	7
β-strand	253-259	7	7
β-strand	265-271	7	7
β-strand	277-279	3	8
β-strand	282-283	2	9
β-strand	286-287	2	9
β-strand	288-291	4	8
β-strand	297-300	4	8
α-helix	312-314	3
β-strand	319	1	10
β-strand	324-326	3	11
β-strand	330-333	4	11
β-strand	338	1	10
β-strand	344	1	10
β-strand	349	1	12
β-strand	350-352	3	11
β-strand	360	1	12
α-helix	362-364	3
β-strand	369	1	13
β-strand	372-374	3	14
β-strand	381-383	3	14
β-strand	386-388	3	13
β-strand	394-396	3	13
β-strand	400-401	2	14
β-strand	424-428	5	15
β-strand	431-435	5	15
β-strand	442-444	3	15
β-strand	445	1	16
β-strand	450	1	16
α-helix	455-457	3
α-helix	458-460	3
β-strand	469-472	4	17
β-strand	475-478	4	17
β-strand	491	1	18
β-strand	494	1	19
β-strand	499	1	19
β-strand	502	1	18
β-strand	515-516	2	7

Chain B: 22 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	5
α-helix	32-35	4
α-helix	36-40	5
β-strand	47-49	3	20
β-strand	50	1	21
β-strand	56-58	3	20
α-helix	60-66	7
α-helix	71-74	4
β-strand	87	1	21
α-helix	93-103	11
β-strand	107-108	2	2
α-helix	117-124	8
α-helix	130-132	3
α-helix	134-138	5
α-helix	144-146	3
α-helix	149-157	9
α-helix	160-163	4
α-helix	168-171	4
α-helix	174-179	6
α-helix	181-184	4
α-helix	188-195	8
β-strand	199-200	2	22
α-helix	201-203	3
α-helix	205-213	9
α-helix	220-222	3
β-strand	233-234	2	22
β-strand	240-243	4	23
β-strand	244-245	2	24
β-strand	252-255	4	24
β-strand	256-257	2	23
β-strand	270-272	3	24
β-strand	277-283	7	25
β-strand	286-291	6	25
β-strand	297-300	4	25
β-strand	310	1	25
α-helix	312-314	3
β-strand	319	1	26
β-strand	322-323	2	27
β-strand	326	1	28
α-helix	327-329	3
β-strand	331	1	28
β-strand	334-335	2	27
β-strand	338	1	26
β-strand	339	1	29
β-strand	343	1	29
β-strand	369	1	30
β-strand	372-376	5	31
β-strand	379-383	5	31
β-strand	385	1	32
β-strand	386	1	30
α-helix	395	1
β-strand	396	1	30
α-helix	397	1
β-strand	401-403	3	31
β-strand	411-412	2	31
β-strand	421	1	32
β-strand	424-428	5	33
β-strand	431-435	5	33
β-strand	442-444	3	33
β-strand	445	1	34
β-strand	450	1	34
β-strand	453	1	33
β-strand	467-472	6	35
β-strand	475-480	6	35
β-strand	492	1	35
β-strand	501	1	35
β-strand	515-517	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Kelch repeat and BTB domain-containing protein 4	A, B	protein	534	Homo sapiens	Q9NVX7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9DTG_1 Isoform 2 of Kelch repeat and BTB domain-containing protein 4 (chains A, B)
MKGGNADSWQREKLASMESPEEPGASMDENYFVNYTFKDRSHSGRVAQGIMKLCLEEELF
ADVTISVEGREFQLHRLVLSAQSCFFRSMFTSNLKEAHNRVIVLQDVSESVFQLLVDYIY
HGTVKLRAEELQEIYEVSDMYQLTSLFEECSRFLARTVQVGNCLQVMWLADRHSDPELYT
AAKHCAKTHLAQLQNTEEFLHLPHRLLTDIISDGVPCSQNPTEAIEAWINFNKEEREAFA
ESLRTSLKEIGENVHIYLIGKESSRTHSLAVSLHCAEDDSISVSGQNSLCHQITAACKHG
GDLYVVGGSIPRRMWKCNNATVDWEWCAPLPRDRLQHTLVSVPGKDAIYSLGGKTLQDTL
SNAVIYYRVGDNVWTETTQLEVAVSGAAGANLNGIIYLLGGEENDLDFFTKPSRLIQCFD
TETDKCHVKPYVLPFAGRMHAAVHKDLVFIVAEGDSLVCYNPLLDSFTRLCLPEAWSSAP
SLWKIASCNGSIYVFRDRYKKGDANTYKLDPATSAVTVTRGIKVLLTNLQFVLA

Primary citation

UM171 glues asymmetric CRL3-HDAC1/2 assembly to degrade CoREST corepressors. Yeo, M.J.R., Zhang, O., Xie, X. et al. Nature (2025) 639:232-240. DOI 10.1038/s41586-024-08532-4 · PubMed

Other PDB entries of the same protein (UniProt Q9NVX7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GGM 2.71 Å, Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex
9DTQ 2.87 Å, The structure of HDAC2-CoREST in complex with KBTBD4R313PRR mutant
9GGN 2.9 Å, Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171
9GGL 3.13 Å, Cryo-EM structure of KBTBD4 WT-HDAC2 2:1 complex mediated by molecular glue UM171
8VPQ 3.3 Å, The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4IPR310delinsTTYML
9I2C 3.3 Å, Cryo-EM structure of KBTBD4 WT-HDAC2-CoREST1 2:1:1 complex mediated by molecular glue…
8VRT 3.42 Å, The structure of LSD1-CoREST-HDAC1 in complex with KBTBD4R313PRR mutant
8VOJ 3.77 Å, The Cryo-EM structure of LSD1-CoREST-HDAC1 in complex with KBTBD4 enhanced by UM171 and…
2EQX Solution structure of the BACK domain of Kelch repeat and BTB domain-containing protein 4

Browse structure collections

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