7VDT: Isoform 2 of Transcription activator BRG1

The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex. Determined by electron microscopy at 2.8 Å resolution. Released 18 May 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Homo sapiens, Xenopus laevis, synthetic construct
Chains: 11
Atoms: 16,704
Mol. weight: 407.75 kDa
Ligands: MG, BEF, ADP
Released: 18 May 2022

Explore 7VDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VDT contains 71 α-helices and 34 β-strands across 9 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: 33 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	543-557	15
α-helix	732-735	4
α-helix	756-770	15
β-strand	776-777	2	1
α-helix	785-798	14
β-strand	807-810	4	1
α-helix	812-814	3
α-helix	815-825	11
β-strand	831-833	3	1
α-helix	838-843	6
α-helix	845-850	6
β-strand	855-859	5	1
α-helix	860-865	6
α-helix	867-870	4
α-helix	874-875	2
β-strand	878-881	4	1
α-helix	883-887	5
α-helix	892-900	9
β-strand	906-909	4	1
α-helix	919-928	10
α-helix	963-971	9
α-helix	981-984	4
β-strand	992-996	5	2
α-helix	999-1001	3
α-helix	1002-1013	12
β-strand	1017-1018	2	3
β-strand	1032-1033	2	3
α-helix	1038-1047	10
α-helix	1049-1052	4
α-helix	1055-1062	8
α-helix	1073-1078	6
α-helix	1080-1094	15
β-strand	1099-1103	5	2
α-helix	1106-1118	13
β-strand	1123-1126	4	2
α-helix	1132-1143	12
β-strand	1151-1155	5	2
α-helix	1156-1159	4
β-strand	1170-1173	4	2
α-helix	1180-1187	8
β-strand	1200-1204	5	2
α-helix	1210-1225	16
α-helix	1226-1230	5
α-helix	1242-1252	11
α-helix	1268-1273	6
α-helix	1277-1294	18
α-helix	1311-1315	5

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	4
α-helix	50-75	26
β-strand	80-81	2	5
α-helix	83-92	10
β-strand	97-98	2	6

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	7
α-helix	46-72	27
β-strand	77-78	2	8
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	9

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	8
α-helix	56-83	28
β-strand	88-89	2	7
α-helix	91-101	11
α-helix	105-123	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
α-helix	64-76	13
β-strand	84	1	10
α-helix	86-113	28
β-strand	118-119	2	11
α-helix	120	1
α-helix	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	11
α-helix	50-75	26
β-strand	81	1	10
α-helix	83-92	10
β-strand	96-98	3	9

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	12
α-helix	46-72	27
β-strand	77-78	2	13
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	6

Chain K: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	47-51	5
α-helix	64-78	15
β-strand	83-84	2	5
α-helix	86-113	28
β-strand	118-119	2	4
α-helix	121-131	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Transcription activator BRG1	A	protein	1485	Homo sapiens	P51532 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)
Histone H3	E, K	protein	136	Xenopus laevis	P84233
DNA (207-mer)	I	DNA	207	synthetic construct
DNA (207-mer)	J	DNA	207	synthetic construct

Sequence of entity 1 (A), FASTA

>7VDT_1 Isoform 2 of Transcription activator BRG1 (chains A)
MQALGQQNRGPTPFNQNQLHQLRAQIMAYKMLARGQPLPDHLQMAVQGKRPMPGMQQQMP
TLPPPSVSATGPGPGPGPGPGPGPGPAPPNYSRPHGMGGPNMPPPGPSGVPPGMPGQPPG
GPPKPWPEGPMANAAAPTSTPQKLIPPQPTGRPSPAPPAVPPAASPVMPPQTQSPGQPAQ
PAPMVPLHQKQSRITPIQKPRGLDPVEILQEREYRLQARIAHRIQELENLPGSLAGDLRT
KATIELKALRLLNFQRQLRQEVVVCMRRDTALETALNAKAYKRSKRQSLREARITEKLEK
QQKIEQERKRRQKHQEYLNSILQHAKDFKEYHRSVTGKIQKLTKAVATYHANTEREQKKE
NERIEKERMRRLMAEDEEGYRKLIDQKKDKRLAYLLQQTDEYVANLTELVRQHKAAQVAK
EKKKKKKKKKAENAEGQTPAIGPDGEPLDETSQMSDLPVKVIHVESGKILTGTDAPKAGQ
LEAWLEMNPGYEVAPRSDSEESGSEEEEEEEEEEQPQAAQPPTLPVEEKKKIPDPDSDDV
SEVDARHIIENAKQDVDDEYGVSQALARGLQSYYAVAHAVTERVDKQSALMVNGVLKQYQ
IKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALITYLMEHKRINGPFLIIVPLSTLSNW
AYEFDKWAPSVVKVSYKGSPAARRAFVPQLRSGKFNVLLTTYEYIIKDKHILAKIRWKYM
IVDEGHRMKNHHCKLTQVLNTHYVAPRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCST
FEQWFNAPFAMTGEKVDLNEEETILIIRRLHKVLRPFLLRRLKKEVEAQLPEKVEYVIKC
DMSALQRVLYRHMQAKGVLLTDGSEKDKKGKGGTKTLMNTIMQLRKICNHPYMFQHIEES
FSEHLGFTGGIVQGLDLYRASGKFELLDRILPKLRATNHKVLLFCQMTSLMTIMEDYFAY
RGFKYLRLDGTTKAEDRGMLLKTFNEPGSEYFIFLLSTRAGGLGLNLQSADTVIIFDSDW
NPHQDLQAQDRAHRIGQQNEVRVLRLCTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKS
SSHERRAFLQAILEHEEQDEEEDEVPDDETVNQMIARHEEEFDLFMRMDLDRRREEARNP
KRKPRLMEEDELPSWIIKDDAEVERLTCEEEEEKMFGRGSRHRKEVDYSDSLTEKQWLKA
IEEGTLEEIEEEVRQKKSSRKRKRDSDAGSSTPTTSTRSRDKDDESKKQKKRGRPPAEKL
SPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIK
ERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDDSE
GEESEEEEEGEEEGSESESRSVKVKIKLGRKEKAQDRLKGGRRRPSRGSRAKPVVSDDDS
EEEQEEDRSGSGSEEDASGGSWSHPQFEKWSHPQFEKWSHPQFEK

Sequence of entity 2 (B, F), FASTA

>7VDT_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>7VDT_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>7VDT_4 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (E, K), FASTA

>7VDT_5 Histone H3 (chains E, K)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 6 (I), FASTA

>7VDT_6 DNA (207-MER) (chains I)
GGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGAAGCTTGTCGAGAA
GTACTAGAGGATCATAATCAGCCATAC

Sequence of entity 7 (J), FASTA

>7VDT_7 DNA (207-MER) (chains J)
GTATGGCTGATTATGATCCTCTAGTACTTCTCGACAAGCTTCAGGATGTATATATCTGAC
ACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTA
CGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGAT
TCTCCAGGGCGGCCGCGTATAGGGTCC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
BEF	Beryllium trifluoride ion	Be F3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Yuan, J.J., Chen, K.J., Zhang, W.B. et al. Nature (2022) 605:166-171. DOI 10.1038/s41586-022-04658-5 · PubMed

Other PDB entries of the same protein (UniProt P51532 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TAB 1.16 Å, G-925 bound to the SMARCA4 (BRG1) Bromodomain
2GRC 1.5 Å, 1.5 A structure of bromodomain from human BRG1 protein, a central ATPase of SWI/SNF…
6ZS2 1.57 Å, Crystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in…
7TD9 1.61 Å, G-059 bound to the SMARCA4 (BRG1) Bromodomain
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
3UVD 1.85 Å, Crystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in…
5DKD 2.0 Å, Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3…
5EA1 2.0 Å, Crystal Structure of SMARCA4 bromodomain in complex with MPD
9DTX 2.11 Å, Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and…
7VRB 2.39 Å, Structure of the Human BRG1/SS18 complex
9UXC 2.74 Å, The ADP-bound structure of BCL7B-containing ARP module of the human SWI/SNF complex
9WBZ 2.9 Å, The structure of NCP-motor-ARP module of ncBAF-nucleosome complex

Browse structure collections

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