4A3F

RNA Polymerase II initial transcribing complex with a 6nt DNA-RNA hybrid and soaked with AMPCPP

Structural Biology Knowledgebase: 4A3F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.156

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4A3F

Classification: TRANSCRIPTION

Total Structure Weight: 529249.81


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 A 1732 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Fragment: RESIDUES 1-1732
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 C 318 Saccharomyces cerevisiae Gene Name(s): RPB3 YIL021W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 D 221 Saccharomyces cerevisiae Gene Name(s): RPB4 YJL140W J0654
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 E 215 Saccharomyces cerevisiae
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 G 171 Saccharomyces cerevisiae Gene Name(s): RPB7 YDR404C D9509.22
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 H 146 Saccharomyces cerevisiae Gene Name(s): RPB8 YOR224C YOR50-14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 I 122 Saccharomyces cerevisiae Gene Name(s): RPB9 YGL070C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 J 70 Saccharomyces cerevisiae Gene Name(s): RPB10 YOR210W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 K 120 Saccharomyces cerevisiae Gene Name(s): RPB11 YOL005C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 L 70 Saccharomyces cerevisiae
Macromolecule Entities
Molecule Chains Length Organism Details
NON TEMPLATE DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP *GP*CP*TP)-3' N 14 Saccharomyces cerevisiae
TRANSCRIPT RNA 5'-R(*CP*CP*AP*GP*GP*AP)-3' P 6 Saccharomyces cerevisiae
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*DTP *TP*TP*CP*C BRU*GP*GP*TP*CP*AP*TP*T)-3' T 26 Saccharomyces cerevisiae

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
APC
Query on APC

A DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, I, J, L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
T DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.156
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 221.60 α = 90.00
b = 391.30 β = 90.00
c = 283.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-30
  • Released Date: 2011-12-07
  • Deposition author(s): Cheung, A.C.M., Sainsbury, S., Cramer, P.

Revision History

  • 2015-05-20
    Type: Source and taxonomy | Details: SOURCE
  • 2011-12-14
    Type: Citation | Details: JRNL