9HYN: SMARCA2-vcb-complex with protac P1

Crystal structure of the SMARCA2-vcb-complex with protac P1. Determined by X-ray diffraction at 2.37 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 2.37 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,619
Mol. weight: 117.72 kDa
Ligands: A1IYO
Released: 22 Oct 2025

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

Secondary structure: helices and β-sheets

9HYN contains 54 α-helices and 58 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: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	10	1	2
β-strand	12-19	8	1
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	1
β-strand	49-50	2	1
α-helix	51-52	2
β-strand	56	1	3
α-helix	57-60	4
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80	1	5
β-strand	85	1	5
α-helix	86-88	3
β-strand	90	1	2
α-helix	91-96	6
α-helix	98-100	3

Chains B and E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	28-32	5	1
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	1
α-helix	67-83	17
α-helix	89-92	4
α-helix	100-110	11

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
α-helix	83	1
β-strand	84-89	6	7
β-strand	95-97	3	7
β-strand	101	1	7
β-strand	106-112	7	6
β-strand	117-121	5	7
β-strand	127	1	7
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	136	1	7
α-helix	142-144	3
α-helix	145-146	2
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-174	3
α-helix	182-189	8
α-helix	194-207	15

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	10	1	9
β-strand	12-19	8	8
β-strand	23	1	10
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	8
β-strand	49-50	2	8
α-helix	51-52	2
β-strand	56	1	10
α-helix	57-60	4
β-strand	68	1	11
β-strand	71	1	11
α-helix	72	1
β-strand	73-79	7	8
β-strand	80-81	2	12
β-strand	84-85	2	12
α-helix	86-88	3
β-strand	90	1	9
α-helix	91-96	6
α-helix	98-100	3

Chain F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
α-helix	83	1
β-strand	84-89	6	13
β-strand	95-97	3	13
β-strand	101	1	13
β-strand	106-112	7	6
β-strand	117-121	5	13
β-strand	127	1	13
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	136	1	13
α-helix	142-144	3
α-helix	145-146	2
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-174	3
α-helix	182-189	8
α-helix	194-202	9

Chains G and H: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1381-1395	15
β-strand	1398	1	14
β-strand	1404	1	14
α-helix	1405-1409	5
α-helix	1412-1414	3
α-helix	1419-1424	6
α-helix	1431-1439	9
α-helix	1446-1464	19
α-helix	1469-1489	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	A, D	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	B, E	protein	103	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	C, F	protein	168	Homo sapiens	P40337 (AlphaFold model)
Isoform Short of Probable global transcription activator SNF2L2	G, H	protein	129	Homo sapiens	P51531 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9HYN_1 Elongin-B (chains A, D)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B, E), FASTA

>9HYN_2 Elongin-C (chains B, E)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDCLELLMA

Sequence of entity 3 (C, F), FASTA

>9HYN_3 von Hippel-Lindau disease tumor suppressor (chains C, F)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGDTQERIA

Sequence of entity 4 (G, H), FASTA

>9HYN_4 Isoform Short of Probable global transcription activator SNF2L2 (chains G, H)
SMAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVD
FKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAK
EEEKSARQK

Ligands and cofactors

ID	Name	Formula	Copies
A1IYO	(2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imi…	C46 H58 Br F N9 O7 S	2

Primary citation

Frustration in the protein-protein interface plays a central role in the cooperativity of PROTAC ternary complexes. Ma, N., Bhattacharya, S., Muk, S. et al. Nat Commun (2025) 16:8595-8595. DOI 10.1038/s41467-025-63713-7 · PubMed

Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex

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