4A3L

RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 7NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP

Structural Biology Knowledgebase: 4A3L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4A3L

Classification: TRANSCRIPTION

Total Structure Weight: 529579.00


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
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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 RPABC1 E 215 Saccharomyces cerevisiae Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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 RPABC3 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 RPABC5 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 RPABC4 L 70 Saccharomyces cerevisiae Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*GP*TP*AP*CP*TP)-3' N 14 Saccharomyces cerevisiae
5'-R(*AP*CP*CP*AP*GP*GP*AP)-3' P 7 Saccharomyces cerevisiae
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP *TP*TP*CP*CP*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

P 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: 0.187
  • R-Value Work: 0.159
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 222.81 α = 90.00
b = 392.44 β = 90.00
c = 279.75 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

  • 2011-12-14
    Type: Citation | Details: JRNL