9KD8 image
Deposition Date 2024-11-03
Release Date 2025-11-12
Last Version Date 2025-11-12
Entry Detail
PDB ID:
9KD8
Keywords:
TRANSCRIPTION
Title:
The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin D.
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288C (Taxon ID: 559292)
synthetic construct (Taxon ID: 32630)
Streptomyces sp. (Taxon ID: 1931)
Host Organism:
Escherichia coli BL21
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.46 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9KD8 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
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 II subunit RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:1224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P16370 Pfam ID:PF01193, PF01000
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P20433 Pfam ID:PF03874
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P20434 Pfam ID:PF03871, PF01191
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P20435 Pfam ID:PF01192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P34087 Pfam ID:PF03876, PF00575
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P20436 Pfam ID:PF03870
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P27999 Pfam ID:PF02150, PF01096
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P22139 Pfam ID:PF01194
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P38902 Pfam ID:PF13656
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288C
UniProt ID:P40422 Pfam ID:PF03604
Polymer Type:polypeptide(L)
Molecule:Actinomycin D
Chain IDs:P (auth: M)
Chain Length:11
Number of Molecules:1
Biological Source:Streptomyces sp.
Polymer Type:polydeoxyribonucleotide
Molecule:NTS(non-template strand)
Chain IDs:M (auth: N)
Chain Length:49
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*CP*CP*CP*UP*AP*AP*GP*AP*GP*UP*AP*C)-3')
Chain IDs:N (auth: P)
Chain Length:12
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:TS(template strand)
Chain IDs:O (auth: T)
Chain Length:49
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
MG
ZN
Peptide-like Molecules
PRD_000001
Primary Citation
The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin D.
To Be Published ? ? ? (?)
Primary Citation of related structures
9KD8
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