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elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP
DOI:10.2210/pdb4by1/pdb   NDB ID: NA2666
4BY1
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transcription
    Structure Weight: 548116.16
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
    Polymer: 1 Type: protein Length: 1733
    Chains: A
    EC#: 2.7.7.6   
    Organism Saccharomyces cerevisiae
    Gene Names RPO21 RPB1 RPB220 SUA8 YDL140C D2150
    UniProtKB:   Protein Feature View | Search PDB | P04050  
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
    Polymer: 2 Type: protein Length: 1224
    Chains: B
    EC#: 2.7.7.6   
    Organism Saccharomyces cerevisiae
    Gene Names RPB2 RPB150 RPO22 YOR151C
    UniProtKB:   Protein Feature View | Search PDB | P08518  
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
    Polymer: 3 Type: protein Length: 318
    Chains: C
    Organism Saccharomyces cerevisiae
    Gene Names RPB3 YIL021W
    UniProtKB:   Protein Feature View | Search PDB | P16370  
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
    Polymer: 4 Type: protein Length: 221
    Chains: D
    Organism Saccharomyces cerevisiae
    Gene Names RPB4 YJL140W J0654
    UniProtKB:   Protein Feature View | Search PDB | P20433  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
    Polymer: 5 Type: protein Length: 215
    Chains: E
    Organism Saccharomyces cerevisiae
    Gene Names RPB5 RPA7 RPC9 YBR154C YBR1204
    UniProtKB:   Protein Feature View | Search PDB | P20434  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
    Polymer: 6 Type: protein Length: 155
    Chains: F
    Organism Saccharomyces cerevisiae
    Gene Names RPO26 RPB6 YPR187W P9677.8
    UniProtKB:   Protein Feature View | Search PDB | P20435  
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
    Polymer: 7 Type: protein Length: 171
    Chains: G
    Organism Saccharomyces cerevisiae
    Gene Names RPB7 YDR404C D9509.22
    UniProtKB:   Protein Feature View | Search PDB | P34087  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
    Polymer: 8 Type: protein Length: 146
    Chains: H
    Organism Saccharomyces cerevisiae
    Gene Names RPB8 YOR224C YOR50-14
    UniProtKB:   Protein Feature View | Search PDB | P20436  
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
    Polymer: 9 Type: protein Length: 122
    Chains: I
    Organism Saccharomyces cerevisiae
    Gene Names RPB9 YGL070C
    UniProtKB:   Protein Feature View | Search PDB | P27999  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
    Polymer: 10 Type: protein Length: 70
    Chains: J
    Organism Saccharomyces cerevisiae
    Gene Names RPB10 YOR210W
    UniProtKB:   Protein Feature View | Search PDB | P22139  
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
    Polymer: 11 Type: protein Length: 120
    Chains: K
    Organism Saccharomyces cerevisiae
    Gene Names RPB11 YOL005C
    UniProtKB:   Protein Feature View | Search PDB | P38902  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
    Polymer: 12 Type: protein Length: 70
    Chains: L
    Organism Saccharomyces cerevisiae
    Gene Names RPC10 RPB12 YHR143W-A YHR143BW
    UniProtKB:   Protein Feature View | Search PDB | P40422  
    Molecule: 5'-D(*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3'
    Polymer: 13 Type: dna Length: 14
    Chains: N
    Organism synthetic construct
    Molecule: 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'
    Polymer: 14 Type: rna Length: 11
    Chains: P
    Organism synthetic construct
    Molecule: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP *TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*AP*T)-3'
    Polymer: 15 Type: dna Length: 26
    Chains: T
    Organism synthetic construct
    Molecule: TRANSCRIPTION FACTOR BYE1
    Polymer: 16 Type: protein Length: 146
    Chains: X
    Fragment: RESIDUES 225-370
    Organism Saccharomyces cerevisiae
    Gene Names BYE1 YKL005C YKL150
    UniProtKB:   Protein Feature View | Search PDB | P36106  
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 6
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 7
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 8
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 9
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 10
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 11
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 12
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 13
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 14
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 15
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 16
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    4BXX  STRUCTURES OF RNA POLYMERASE II COMPLEXES WITH BYE1, A CHROMATIN-BINDING PHF3 DIDO HOMOLOGUE 
    4BXY  ELONGATING RNA POLYMERASE II-BYE1 TLD COMPLEX 
    4BXZ  RNA POLYMERASE II-BYE1 COMPLEX 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    APC
    Search 
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    APC C11 H18 N5 O12 P3
    DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
    MG
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    MG Mg
    MAGNESIUM ION
    ZN
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    ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    BRU
    Search 
    BRU C9 H12 Br N2 O8 P DU dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2666
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PQS (software)
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