7ZSA image
Deposition Date 2022-05-06
Release Date 2022-11-16
Last Version Date 2025-07-02
Entry Detail
PDB ID:
7ZSA
Keywords:
TRANSCRIPTION
Title:
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B)
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae (Taxon ID: 4932)
Xenopus laevis (Taxon ID: 8355)
synthetic construct (Taxon ID: 32630)
Expression System(s):
Saccharomyces cerevisiae, Escherichia coli, Trichoplusia ni
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7ZSA validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):RAD3
Chain IDs:W (auth: 0)
Chain Length:778
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06839 Pfam ID:PF06733, PF06777, PF13307 EC:3.6.4.12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB1
Chain IDs:X (auth: 1)
Chain Length:645
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32776 Pfam ID:PF08567, PF03909
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB2
Chain IDs:Y (auth: 2)
Chain Length:517
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02939 Pfam ID:PF03849, PF18307
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II transcripti
Gene (Uniprot):TFB3
Chain IDs:Z (auth: 3)
Chain Length:324
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q03290 Pfam ID:PF17121, PF06391
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB4
Chain IDs:AA (auth: 4)
Chain Length:341
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12004 Pfam ID:PF03850
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):TFB5
Chain IDs:BA (auth: 5)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7C1 Pfam ID:PF06331
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):SSL1
Chain IDs:CA (auth: 6)
Chain Length:464
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04673 Pfam ID:PF04056, PF07975
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA
Gene (Uniprot):SSL2
Chain IDs:DA (auth: 7)
Chain Length:843
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q00578 Pfam ID:PF13625, PF04851, PF16203 EC:3.6.4.12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04050 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001 EC:2.7.7.6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:102
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560 EC:2.7.7.6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P16370 Pfam ID:PF01193, PF01000
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20433 Pfam ID:PF03874
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20434 Pfam ID:PF03871, PF01191
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20435 Pfam ID:PF01192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:177
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P34087 Pfam ID:PF03876, PF00575
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20436 Pfam ID:PF03870
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P27999 Pfam ID:PF02150, PF01096
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22139 Pfam ID:PF01194
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38902 Pfam ID:PF13656
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40422 Pfam ID:PF03604
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):SUA7
Chain IDs:M
Chain Length:352
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P29055 Pfam ID:PF08271, PF00382
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template DNA (209-MER)
Chain IDs:N
Chain Length:209
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):SPT15
Chain IDs:O
Chain Length:247
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P13393 Pfam ID:PF00352
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFG1
Chain IDs:P (auth: Q)
Chain Length:738
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41895 Pfam ID:PF05793
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFG2
Chain IDs:Q (auth: R)
Chain Length:400
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41896 Pfam ID:PF17683, PF02270
Polymer Type:polydeoxyribonucleotide
Molecule:Template DNA (209-MER)
Chain IDs:R (auth: T)
Chain Length:209
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Chain IDs:S (auth: U)
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32773 Pfam ID:PF03153
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TOA2
Chain IDs:T (auth: V)
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32774 Pfam ID:PF02268, PF02751
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFA1
Chain IDs:U (auth: W)
Chain Length:492
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36100 Pfam ID:PF02002
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):TFA2
Chain IDs:V (auth: X)
Chain Length:328
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36145 Pfam ID:PF02186, PF18121, PF22254
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:EA (auth: a), IA (auth: e)
Chain Length:135
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:FA (auth: b), JA (auth: f)
Chain Length:155
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A
Chain IDs:GA (auth: c), KA (auth: g)
Chain Length:129
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:HA (auth: d), LA (auth: h)
Chain Length:221
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Ligand Molecules
MG
SF4
ZN
Primary Citation
Structures of transcription preinitiation complex engaged with the +1 nucleosome.
Nat. Struct. Mol. Biol. 30 226 232 (2023)
PMID: 36411341 DOI: 10.1038/s41594-022-00865-w

Abstact

The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.

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Disease

Primary Citation of related structures
7ZSA
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