ISDA

Deposition Date 2006-11-13

Release Date 2006-12-12

Last Version Date 2023-10-25

Entry Detail

PDB ID:

2NVQ

Keywords:

TRANSCRIPTION,TRANSFERASE/DNA-RNA HYBRID

Title:

RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)
Saccharomyces cerevisiae (Taxon ID: 4932)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.90 Å

R-Value Free:

0.28

R-Value Work:

0.22

R-Value Observed:

0.23

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II largest subunit
Gene (Uniprot):RPO21
Chain IDs:D (auth: 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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 140 kDa polypeptide
Gene (Uniprot):RPB2
Chain IDs:E (auth: B)
Chain Length:1224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 45 kDa polypeptide
Gene (Uniprot):RPB3
Chain IDs:F (auth: C)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P16370 Pfam ID:PF01193, PF01000

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Gene (Uniprot):RPB5
Chain IDs:G (auth: E)
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20434 Pfam ID:PF03871, PF01191

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Gene (Uniprot):RPO26
Chain IDs:H (auth: F)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20435 Pfam ID:PF01192

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Gene (Uniprot):RPB8
Chain IDs:I (auth: H)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20436 Pfam ID:PF03870

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit 9
Gene (Uniprot):RPB9
Chain IDs:J (auth: I)
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P27999 Pfam ID:PF02150, PF01096

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I/II/III subunit 10
Gene (Uniprot):RPB10
Chain IDs:K (auth: J)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P22139 Pfam ID:PF01194

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II 13.6 kDa polypeptide
Gene (Uniprot):RPB11
Chain IDs:L (auth: K)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38902 Pfam ID:PF13656

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Gene (Uniprot):RPC10
Chain IDs:M (auth: L)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P40422 Pfam ID:PF03604

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3'
Chain IDs:C (auth: N)
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'
Chain IDs:A (auth: R)
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:28-MER DNA template strand
Chain IDs:B (auth: T)
Chain Length:28
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

DUT

Primary Citation

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis

Wang, D, Bushnell, D.A, Westover, K.D, Kaplan, C.D, Kornberg, R.D.Show

Cell(Cambridge,Mass.) 127 941 954 (2006)

PMID: 17129781 DOI: 10.1016/j.cell.2006.11.023

Abstact

New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.

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Protein

Chemical

Disease

Primary Citation of related structures