8QJR: BRG1 bromodomain

BRG1 bromodomain in complex with VBC via compound 17. Determined by X-ray diffraction at 3.17 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 3.17 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,553
Mol. weight: 114.24 kDa
Ligands: PO4, VLH
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8QJR contains 55 α-helices and 62 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: 7 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	43-45	3	1
β-strand	50	1	1
α-helix	51-52	2
β-strand	56	1	3
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-78	6	1
β-strand	80-81	2	5
β-strand	84-85	2	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: 4 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	97-110	14

Chains C and F: 9 helices, 13 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
α-helix	99-100	2
β-strand	101	1	7
α-helix	102	1
β-strand	106-112	7	6
β-strand	116-121	6	7
β-strand	127	1	7
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	135-136	2	7
α-helix	142-144	3
α-helix	145-146	2
β-strand	147-152	6	6
β-strand	156	1	8
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-210	17
β-strand	211	1	9

Chain D: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	10
β-strand	10	1	11
β-strand	12-19	8	10
β-strand	23	1	12
α-helix	24-35	12
α-helix	39-41	3
β-strand	43-45	3	10
β-strand	50	1	10
α-helix	51-52	2
β-strand	56	1	12
β-strand	68	1	13
β-strand	71	1	13
α-helix	72	1
β-strand	73-78	6	10
β-strand	80-81	2	14
β-strand	84-85	2	14
α-helix	86-88	3
β-strand	90	1	11
α-helix	91-100	10

Chain G: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1458-1471	14
β-strand	1473	1	17
β-strand	1480	1	17
α-helix	1483-1485	3
α-helix	1488-1490	3
α-helix	1495-1500	6
α-helix	1507-1515	9
α-helix	1522-1539	18
α-helix	1541	1
α-helix	1545-1565	21

Chain H: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1458-1471	14
β-strand	1473	1	18
β-strand	1480	1	18
α-helix	1483-1485	3
α-helix	1488-1490	3
α-helix	1495-1500	6
α-helix	1507-1515	9
α-helix	1522-1539	18
α-helix	1541	1
α-helix	1545-1558	14

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	97	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	C, F	protein	162	Homo sapiens	P40337 (AlphaFold model)
Transcription activator BRG1	G, H	protein	121	Homo sapiens	P51532 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8QJR_1 Elongin-B (chains A, D)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B, E), FASTA

>8QJR_2 Elongin-C (chains B, E)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C, F), FASTA

>8QJR_3 von Hippel-Lindau disease tumor suppressor (chains C, F)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 4 (G, H), FASTA

>8QJR_4 Transcription activator BRG1 (chains G, H)
SMLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFK
KIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKED
D

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	7
VLH	(2S,4R)-1-[(2R)-2-[3-[2-[4-[3-[4-[(1R,5S)-3-[3-azanyl-6-(2-hydroxyphenyl)pyrida…	C57 H69 N11 O8 S	2

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. Berlin, M., Cantley, J., Bookbinder, M. et al. J Med Chem (2024) 67:1262-1313. DOI 10.1021/acs.jmedchem.3c01781 · 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

Browse structure collections

About this viewer

MolViewer shows 8QJR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.