9GGM: KBTBD4 P313PRR mutant-HDAC2 2:2 complex

Name: PDB 9GGM: Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex
Published: 2025-04-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of KBTBD4 P313PRR mutant-HDAC2 2:2 complex. Determined by electron microscopy at 2.71 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.71 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,460
Mol. weight: 227.94 kDa
Ligands: ZN
Released: 9 Apr 2025

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

Secondary structure: helices and β-sheets

9GGM contains 63 α-helices and 106 β-strands across 4 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: 15 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	1
α-helix	42-56	15
α-helix	77-80	4
α-helix	84-89	6
α-helix	109-120	12
β-strand	123-125	3	2
α-helix	128-130	3
α-helix	131-140	10
α-helix	145-154	10
α-helix	163-173	11
α-helix	178-188	11
α-helix	205-213	9
α-helix	221-226	6
β-strand	258-260	3	3
α-helix	269	1
β-strand	270-275	6	3
β-strand	281-287	7	3
β-strand	293-296	4	4
β-strand	299	1	5
β-strand	302	1	5
β-strand	304-307	4	4
β-strand	315-318	4	4
β-strand	327-328	2	4
α-helix	330-332	3
β-strand	336-337	2	6
β-strand	340-344	5	7
β-strand	349-353	5	7
β-strand	356-357	2	6
β-strand	362	1	6
β-strand	366-370	5	7
β-strand	375-379	5	7
α-helix	380-382	3
β-strand	387	1	8
α-helix	389	1
β-strand	390-394	5	9
β-strand	397-401	5	9
β-strand	404-407	4	8
β-strand	411-414	4	8
β-strand	418-422	5	9
β-strand	427-430	4	9
β-strand	441-442	2	10
β-strand	445-446	2	10
β-strand	449-454	6	10
β-strand	459-462	4	10
β-strand	469-471	3	10
β-strand	486-489	4	11
β-strand	494-497	4	11
β-strand	500	1	12
β-strand	508-511	4	11
β-strand	518-520	3	11
β-strand	530	1	12
β-strand	531-534	4	3

Chains B and D: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	28
α-helix	18-22	5
α-helix	35-46	12
α-helix	48-51	4
β-strand	53-55	3	28
α-helix	57-61	5
α-helix	62-65	4
α-helix	71-79	9
α-helix	91-94	4
α-helix	107-114	8
α-helix	116-126	11
β-strand	132-135	4	28
β-strand	149	1	29
β-strand	152	1	29
α-helix	156-165	10
β-strand	171-176	6	28
α-helix	182-187	6
β-strand	194-201	8	28
β-strand	217	1	30
β-strand	220	1	30
β-strand	226-229	4	28
α-helix	235-253	19
β-strand	258-263	6	28
α-helix	264-266	3
β-strand	267	1	31
β-strand	277	1	31
α-helix	279-291	13
β-strand	296-301	6	28
α-helix	306-321	16
β-strand	328	1	32
α-helix	335-338	4
β-strand	343	1	32
α-helix	357-371	15

Chain C: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	2
α-helix	42-56	15
α-helix	77-80	4
α-helix	84-89	6
α-helix	109-120	12
β-strand	123-125	3	1
α-helix	128-130	3
α-helix	131-140	10
α-helix	145-154	10
α-helix	163-173	11
α-helix	178-188	11
α-helix	205-213	9
α-helix	221-226	6
β-strand	258-260	3	18
β-strand	270-275	6	18
β-strand	281-287	7	18
β-strand	293-299	7	19
β-strand	302-307	6	19
β-strand	315-318	4	19
β-strand	327-328	2	19
α-helix	330-332	3
β-strand	336-337	2	20
β-strand	340-344	5	21
β-strand	349-353	5	21
β-strand	356-357	2	20
β-strand	362	1	20
β-strand	363	1	22
β-strand	366-370	5	21
β-strand	375-379	5	21
α-helix	380-382	3
β-strand	386	1	22
β-strand	387	1	23
α-helix	389	1
β-strand	390-394	5	24
β-strand	397-401	5	24
β-strand	404-407	4	23
β-strand	411-414	4	23
β-strand	418-422	5	24
β-strand	427-430	4	24
β-strand	441-442	2	25
β-strand	445-446	2	25
β-strand	449-454	6	25
β-strand	459-462	4	25
β-strand	469-471	3	25
β-strand	486-489	4	26
β-strand	494-497	4	26
β-strand	500	1	27
β-strand	508-511	4	26
β-strand	518-520	3	26
β-strand	530	1	27
β-strand	531-534	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 1 of Kelch repeat and BTB domain-containing protein 4	A, C	protein	520	Homo sapiens	Q9NVX7 (AlphaFold model)
Histone deacetylase 2	B, D	protein	488	Homo sapiens	Q92769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9GGM_1 Isoform 1 of Kelch repeat and BTB domain-containing protein 4 (chains A, C)
MESPEEPGASMDENYFVNYTFKDRSHSGRVAQGIMKLCLEEELFADVTISVEGREFQLHR
LVLSAQSCFFRSMFTSNLKEAHNRVIVLQDVSESVFQLLVDYIYHGTVKLRAEELQEIYE
VSDMYQLTSLFEECSRFLARTVQVGNCLQVMWLADRHSDPELYTAAKHCAKTHLAQLQNT
EEFLHLPHRLLTDIISDGVPCSQNPTEAIEAWINFNKEEREAFAESLRTSLKEIGENVHI
YLIGKESSRTHSLAVSLHCAEDDSISVSGQNSLCHQITAACKHGGDLYVVGGSIPRPRRM
WKCNNATVDWEWCAPLPRDRLQHTLVSVPGKDAIYSLGGKTLQDTLSNAVIYYRVGDNVW
TETTQLEVAVSGAAGANLNGIIYLLGGEENDLDFFTKPSRLIQCFDTETDKCHVKPYVLP
FAGRMHAAVHKDLVFIVAEGDSLVCYNPLLDSFTRLCLPEAWSSAPSLWKIASCNGSIYV
FRDRYKKGDANTYKLDPATSAVTVTRGIKVLLTNLQFVLA

Sequence of entity 2 (B, D), FASTA

>9GGM_2 Histone deacetylase 2 (chains B, D)
MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEE
FSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGT
KSEQLSNP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural mimicry of UM171 and neomorphic cancer mutants co-opts E3 ligase KBTBD4 for HDAC1/2 recruitment. Chen, Z., Chi, G., Balo, T. et al. Nat Commun (2025) 16:3144-3144. DOI 10.1038/s41467-025-58350-z · PubMed

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

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…
9DTG 3.83 Å, The cryo-EM structure of apo KBTBD4
2EQX Solution structure of the BACK domain of Kelch repeat and BTB domain-containing protein 4

Browse structure collections

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