Assemblies
Assembly Name:
DNA-directed RNA polymerase II complex and RNA and DNA
Multimeric state:
hetero pentadecamer
Accessible surface area:
156522.32 Å2
Buried surface area:
71303.09 Å2
Dissociation area:
1,690.61
Å2
Dissociation energy (ΔGdiss):
7.46
kcal/mol
Dissociation entropy (TΔSdiss):
11.26
kcal/mol
Symmetry number:
1
PDBe Complex ID:
PDB-CPX-116371
Macromolecules
Chain: A
Length: 1733 amino acids
Theoretical weight: 191.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
Length: 1733 amino acids
Theoretical weight: 191.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P04050 (Residues: 1-1733; Coverage: 100%)
Pfam:
- RNA polymerase Rpb1, domain 1
- RNA polymerase Rpb1, domain 2
- RNA polymerase Rpb1, domain 3
- RNA polymerase Rpb1, domain 4
- RNA polymerase Rpb1, domain 5
- RNA polymerase Rpb1, domain 6
- RNA polymerase Rpb1, domain 7
- RNA polymerase Rpb1 C-terminal repeat
- RNA polymerase Rpb1, clamp domain superfamily
- RNA polymerase Rpb1, domain 1
- DNA-directed RNA polymerase, subunit beta-prime
- RNA polymerase, N-terminal
- RNA polymerase, alpha subunit
- RNA polymerase Rpb1, domain 3
- RNA polymerase Rpb1, domain 3 superfamily
- RNA polymerase Rpb1, funnel domain superfamily
- RNA polymerase Rpb1, domain 4
- RNA polymerase Rpb1, domain 5
- RNA polymerase Rpb1, domain 6
- RNA polymerase Rpb1, domain 7
- RNA polymerase Rpb1, domain 7 superfamily
- RNA polymerase II, heptapeptide repeat, eukaryotic
Chain: B
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P08518 (Residues: 1-1224; Coverage: 100%)
Pfam:
- RNA polymerase beta subunit
- RNA polymerase Rpb2, domain 2
- RNA polymerase Rpb2, domain 3
- RNA polymerase Rpb2, domain 4
- RNA polymerase Rpb2, domain 5
- RNA polymerase Rpb2, domain 6
- RNA polymerase Rpb2, domain 7
- DNA-directed RNA polymerase, subunit 2
- RNA polymerase, beta subunit, protrusion
- RNA polymerase Rpb2, domain 2
- RNA polymerase Rpb2, domain 2 superfamily
- RNA polymerase Rpb2, domain 3
- RNA polymerase Rpb2, domain 4
- RNA polymerase Rpb2, domain 5
- DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
- DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
- RNA polymerase Rpb2, OB-fold
- RNA polymerase, beta subunit, conserved site
- RNA polymerase Rpb2, domain 7
Chain: C
Length: 347 amino acids
Theoretical weight: 38.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
InterPro:
Length: 347 amino acids
Theoretical weight: 38.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P16370 (Residues: 2-318; Coverage: 100%)
Pfam:
InterPro:
- RNA polymerase, RBP11-like subunit
- DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1
- DNA-directed RNA polymerase, RpoA/D/Rpb3-type
- DNA-directed RNA polymerase, 30-40kDa subunit, conserved site
- DNA-directed RNA polymerase, insert domain superfamily
- DNA-directed RNA polymerase, insert domain
Chain: D
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam: RNA polymerase Rpb4
InterPro:
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Pfam: RNA polymerase Rpb4
InterPro:
- DNA-directed RNA polymerase II subunit Rpb4-like
- HRDC-like superfamily
- RNA polymerase subunit Rpb4/RPC9
- Rpb4/RPC9 superfamily
- RNA polymerase Rpb4/RPC9, core
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
InterPro:
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Pfam:
InterPro:
- DNA-directed RNA polymerase subunit Rpo5/Rpb5
- RNA polymerase Rpb5, N-terminal domain superfamily
- RNA polymerase, Rpb5, N-terminal
- RPB5-like RNA polymerase subunit superfamily
- RNA polymerase, subunit H/Rpb5 C-terminal
- RNA polymerase, subunit H/Rpb5, conserved site
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam: RNA polymerase Rpb6
InterPro:
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Pfam: RNA polymerase Rpb6
InterPro:
- Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit
- DNA-directed RNA polymerase, subunit RPB6
- RPB6/omega subunit-like superfamily
- RNA polymerase, subunit omega/Rpo6/RPB6
- DNA-directed RNA polymerase, 14-18kDa subunit, conserved site
Chain: G
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
InterPro:
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Pfam:
InterPro:
- RNA polymerase Rpb7-like, N-terminal domain superfamily
- RNA polymerase subunit Rpb7-like
- RNA polymerase Rpb7-like , N-terminal
- S1 domain
- Nucleic acid-binding, OB-fold
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam: RNA polymerase Rpb8
InterPro:
CATH: Nucleic acid-binding proteins
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Pfam: RNA polymerase Rpb8
InterPro:
CATH: Nucleic acid-binding proteins
Chain: I
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
InterPro:
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Pfam:
InterPro:
- DNA-directed RNA polymerase subunit/transcription factor S
- DNA-directed RNA polymerase, M/15kDa subunit
- DNA-directed RNA polymerase M, 15kDa subunit, conserved site
- Pol II subunit B9, C-terminal zinc ribbon
- Zinc finger, TFIIS-type
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
- DNA-directed RNA polymerase subunit RPABC5/Rpb10
- RNA polymerase subunit RPB10
- RNA polymerases, subunit N, zinc binding site
Chain: K
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam:
InterPro:
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Pfam:
InterPro:
- RNA polymerase, RBP11-like subunit
- RNA polymerase RBP11
- DNA-directed RNA polymerase subunit Rpo11-like
- DNA-directed RNA polymerase, RBP11-like dimerisation domain
- DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site
Chain: L
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
- Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
- DNA-directed RNA polymerases I, II, and III subunit RPABC4
- RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4
- RNA polymerase subunit RPABC4/transcription elongation factor Spt4
Name:
5'-D(*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3'
Representative chains: N
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Representative chains: N
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Name:
5'-D(*AP*GP*CP*TP*C*AP*AP*GP*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3'
Representative chains: T
Length: 26 nucleotides
Theoretical weight: 8.03 KDa
Representative chains: T
Length: 26 nucleotides
Theoretical weight: 8.03 KDa
Name:
5'-R(*UP*GP*CP*AP*UP*UP*U*CP*AP*AP*CP*CP*AP*GP*GP*CP*UP*G)-3'
Representative chains: P
Length: 18 nucleotides
Theoretical weight: 5.71 KDa
Representative chains: P
Length: 18 nucleotides
Theoretical weight: 5.71 KDa