9GGN: PDB entry 9GGN

Name: PDB 9GGN: Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171
Published: 2025-04-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of KBTBD4 WT-HDAC2 2:2 complex mediated by molecular glue UM171. Determined by electron microscopy at 2.9 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,936
Mol. weight: 228.34 kDa
Ligands: A1ACV, ZN
Released: 9 Apr 2025

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

Secondary structure: helices and β-sheets

9GGN contains 52 α-helices and 88 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: 9 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	1
α-helix	41-52	12
β-strand	65-67	3	2
β-strand	70-72	3	2
α-helix	84-89	6
α-helix	109-121	13
β-strand	124-127	4	3
α-helix	128-130	3
α-helix	131-140	10
α-helix	144-157	14
α-helix	176-184	9
β-strand	293-297	5	4
β-strand	304-307	4	4
β-strand	314-316	3	4
α-helix	328-330	3
β-strand	335	1	5
β-strand	338-342	5	6
α-helix	343-345	3
β-strand	347-351	5	6
β-strand	353-354	2	5
β-strand	360-361	2	5
β-strand	365-368	4	6
β-strand	373-376	4	6
β-strand	385	1	7
β-strand	388-392	5	8
β-strand	395-399	5	8
β-strand	402-405	4	7
β-strand	409-412	4	7
β-strand	416-420	5	8
β-strand	425-428	4	8
β-strand	440-444	5	9
β-strand	447-451	5	9
β-strand	457-460	4	9
β-strand	461	1	10
β-strand	466	1	10
β-strand	483-485	3	11
β-strand	493	1	12
β-strand	494-496	3	11
β-strand	508	1	12
β-strand	509-510	2	13
β-strand	515-516	2	13

Chains B and D: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	14
α-helix	20-22	3
α-helix	35-40	6
α-helix	43-45	3
α-helix	47-49	3
β-strand	53-55	3	14
α-helix	62-65	4
α-helix	71-77	7
α-helix	89-92	4
β-strand	97	1	15
β-strand	101	1	15
α-helix	107-126	20
β-strand	132-135	4	14
β-strand	149	1	16
β-strand	152	1	16
α-helix	156-167	12
β-strand	171-175	5	14
α-helix	183-186	4
β-strand	194-201	8	14
α-helix	218-220	3
β-strand	224-229	6	14
α-helix	235-253	19
β-strand	257-262	6	14
α-helix	279-282	4
α-helix	290-292	3
β-strand	296-300	5	14
α-helix	306-321	16
α-helix	324-326	3
α-helix	357-371	15

Chain C: 9 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	3
α-helix	41-52	12
β-strand	65-67	3	17
β-strand	70-72	3	17
α-helix	84-89	6
α-helix	109-121	13
β-strand	124-127	4	1
α-helix	128-130	3
α-helix	131-140	10
α-helix	144-157	14
α-helix	176-184	9
β-strand	293-297	5	18
β-strand	304-307	4	18
β-strand	314-316	3	18
α-helix	328-330	3
β-strand	335	1	19
β-strand	338-342	5	20
α-helix	343-345	3
β-strand	347-351	5	20
β-strand	353-354	2	19
β-strand	360-361	2	19
β-strand	365-368	4	20
β-strand	373-376	4	20
β-strand	385	1	21
β-strand	388-392	5	22
β-strand	395-399	5	22
β-strand	402-405	4	21
β-strand	409-412	4	21
β-strand	416-420	5	22
β-strand	425-429	5	22
β-strand	440-444	5	23
β-strand	447-451	5	23
β-strand	457-460	4	23
β-strand	461	1	24
β-strand	466	1	24
β-strand	483-485	3	25
β-strand	493	1	26
β-strand	494-496	3	25
β-strand	508	1	26
β-strand	509-510	2	27
β-strand	515-516	2	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 1 of Kelch repeat and BTB domain-containing protein 4	A, C	protein	518	Homo sapiens	Q9NVX7 (AlphaFold model)
Histone deacetylase 2	B, D	protein	488	Homo sapiens	Q92769 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9GGN_1 Isoform 1 of Kelch repeat and BTB domain-containing protein 4 (chains A, C)
MESPEEPGASMDENYFVNYTFKDRSHSGRVAQGIMKLCLEEELFADVTISVEGREFQLHR
LVLSAQSCFFRSMFTSNLKEAHNRVIVLQDVSESVFQLLVDYIYHGTVKLRAEELQEIYE
VSDMYQLTSLFEECSRFLARTVQVGNCLQVMWLADRHSDPELYTAAKHCAKTHLAQLQNT
EEFLHLPHRLLTDIISDGVPCSQNPTEAIEAWINFNKEEREAFAESLRTSLKEIGENVHI
YLIGKESSRTHSLAVSLHCAEDDSISVSGQNSLCHQITAACKHGGDLYVVGGSIPRRMWK
CNNATVDWEWCAPLPRDRLQHTLVSVPGKDAIYSLGGKTLQDTLSNAVIYYRVGDNVWTE
TTQLEVAVSGAAGANLNGIIYLLGGEENDLDFFTKPSRLIQCFDTETDKCHVKPYVLPFA
GRMHAAVHKDLVFIVAEGDSLVCYNPLLDSFTRLCLPEAWSSAPSLWKIASCNGSIYVFR
DRYKKGDANTYKLDPATSAVTVTRGIKVLLTNLQFVLA

Sequence of entity 2 (B, D), FASTA

>9GGN_2 Histone deacetylase 2 (chains B, D)
MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEE
FSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGT
KSEQLSNP

Ligands and cofactors

ID	Name	Formula	Copies
A1ACV	(1r,4r)-N~1~-[(7P)-2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]ind…	C25 H27 N9	2
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:

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
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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