8BVW image
Deposition Date 2022-12-20
Release Date 2023-05-03
Last Version Date 2024-07-24
Entry Detail
PDB ID:
8BVW
Keywords:
TRANSCRIPTION
Title:
RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Xenopus laevis (Taxon ID: 8355)
unidentified adenovirus (Taxon ID: 10535)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Trichoplusia ni
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8BVW validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH helicase subunit XPB
Gene (Uniprot):ERCC3
Mutations:0
Chain IDs:A (auth: 0)
Chain Length:772
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P19447 Pfam ID:PF13625, PF04851, PF16203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TFIIH basal transcription factor complex helicase XPD subunit
Gene (Uniprot):ERCC2
Mutations:0
Chain IDs:B (auth: 1)
Chain Length:760
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18074 Pfam ID:PF06733, PF06777, PF13307 EC:3.6.4.12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 1
Gene (Uniprot):GTF2H1
Mutations:0
Chain IDs:C (auth: 2)
Chain Length:548
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P32780 Pfam ID:PF08567, PF03909
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 4
Gene (Uniprot):GTF2H4
Mutations:0
Chain IDs:D (auth: 3)
Chain Length:462
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92759 Pfam ID:PF03849, PF18307
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 2
Gene (Uniprot):GTF2H2
Mutations:0
Chain IDs:E (auth: 4)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13888 Pfam ID:PF04056, PF07975
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 3
Gene (Uniprot):GTF2H3
Mutations:0
Chain IDs:F (auth: 5)
Chain Length:308
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13889 Pfam ID:PF03850
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 5
Gene (Uniprot):GTF2H5
Mutations:0
Chain IDs:G (auth: 6)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6ZYL4 Pfam ID:PF06331
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CDK-activating kinase assembly factor MAT1
Gene (Uniprot):MNAT1
Mutations:0
Chain IDs:H (auth: 7)
Chain Length:309
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P51948 Pfam ID:PF17121, PF06391
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cyclin-dependent kinase 7
Gene (Uniprot):CDK7
Mutations:0
Chain IDs:I (auth: 8)
Chain Length:346
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P50613 Pfam ID:PF00069 EC:2.7.11.22
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cyclin-H
Gene (Uniprot):CCNH
Mutations:0
Chain IDs:J (auth: 9)
Chain Length:323
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P51946 Pfam ID:PF00134, PF16899
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Mutations:0
Chain IDs:K (auth: A)
Chain Length:1970
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A7M4DUC2 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):POLR2B
Chain IDs:L (auth: B)
Chain Length:103
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LGP4 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):POLR2C
Chain IDs:M (auth: C)
Chain Length:130
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LCH3 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit D
Gene (Uniprot):POLR2D
Chain IDs:N (auth: D)
Chain Length:126
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287ADR4 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit E
Gene (Uniprot):POLR2E
Chain IDs:O (auth: E)
Chain Length:136
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LSI7 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit F
Chain IDs:P (auth: F)
Chain Length:127
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VEK9 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):POLR2G
Chain IDs:Q (auth: G)
Chain Length:172
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VKG7 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):POLR2H
Chain IDs:R (auth: H)
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LCB2 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):POLR2I
Chain IDs:S (auth: I)
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:P60899 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):POLR2L
Chain IDs:T (auth: J)
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VYD0 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11-a
Gene (Uniprot):POLR2J
Chain IDs:U (auth: K)
Chain Length:117
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RKE4 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit K
Chain IDs:V (auth: L)
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TRS6 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIB
Gene (Uniprot):GTF2B
Chain IDs:W (auth: M)
Chain Length:316
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q00403 Pfam ID:PF08271, PF00382
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template DNA
Chain IDs:X (auth: N)
Chain Length:218
Number of Molecules:1
Biological Source:unidentified adenovirus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):TBP
Chain IDs:Y (auth: O)
Chain Length:339
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P20226 Pfam ID:PF00352
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 1
Gene (Uniprot):GTF2F1
Chain IDs:Z (auth: Q)
Chain Length:517
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35269 Pfam ID:PF05793
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 2
Gene (Uniprot):GTF2F2
Chain IDs:AA (auth: R)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P13984 Pfam ID:PF17683, PF02270
Polymer Type:polydeoxyribonucleotide
Molecule:Template DNA
Chain IDs:BA (auth: T)
Chain Length:218
Number of Molecules:1
Biological Source:unidentified adenovirus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 1
Gene (Uniprot):GTF2A1
Chain IDs:CA (auth: U)
Chain Length:376
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52655 Pfam ID:PF03153
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 2
Gene (Uniprot):GTF2A2
Chain IDs:DA (auth: V)
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52657 Pfam ID:PF02268, PF02751
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIE subunit 1
Gene (Uniprot):GTF2E1
Chain IDs:EA (auth: W)
Chain Length:439
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P29083 Pfam ID:PF02002, PF08271, PF11521
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit beta
Gene (Uniprot):GTF2E2
Chain IDs:FA (auth: X)
Chain Length:291
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P29084 Pfam ID:PF02186, PF18121
Polymer Type:polypeptide(L)
Molecule:Unassigned peptide, likely XPB
Chain IDs:GA (auth: Y)
Chain Length:8
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Unassigned peptide, likely TFIIE-beta
Chain IDs:HA (auth: Z)
Chain Length:19
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Mutations:G103A
Chain IDs:IA (auth: a), MA (auth: e)
Chain Length:1970
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Mutations:0
Chain IDs:JA (auth: b), NA (auth: f)
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:KA (auth: c), OA (auth: g)
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:LA (auth: d), PA (auth: h)
Chain Length:126
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Ligand Molecules
MG
SF4
ZN
Primary Citation
Structural basis of transcription reduction by a promoter-proximal +1 nucleosome.
Mol.Cell 83 1798 ? (2023)
PMID: 37148879 DOI: 10.1016/j.molcel.2023.04.011

Abstact

At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.

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Protein

Chemical

Disease

Primary Citation of related structures
8BZ1
8BYQ