1Y1V image
Deposition Date 2004-11-19
Release Date 2004-12-28
Last Version Date 2024-03-13
Entry Detail
PDB ID:
1Y1V
Title:
Refined RNA Polymerase II-TFIIS complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.80 Å
R-Value Free:
0.29
R-Value Work:
0.28
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II largest subunit
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 140 kDa polypeptide
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:1224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 45 kDa polypeptide
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 32 kDa polypeptide
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 19 kDa polypeptide
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit 9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I/II/III subunit 10
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 13.6 kDa polypeptide
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor S-II
Gene (Uniprot):DST1
Chain IDs:M (auth: S)
Chain Length:179
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
Mol.Cell 16 955 965 (2004)
PMID: 15610738 DOI: 10.1016/j.molcel.2004.11.040

Abstact

The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.

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Primary Citation of related structures