4BY1

elongating RNA Polymerase II-Bye1 TLD complex soaked with AMPCPP

Structural Biology Knowledgebase: 4BY1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4BY1

Classification: TRANSCRIPTION

Total Structure Weight: 548116.16


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 C 318 Saccharomyces cerevisiae Gene Name(s): RPB3 YIL021W
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 D 221 Saccharomyces cerevisiae Gene Name(s): RPB4 YJL140W J0654
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 E 215 Saccharomyces cerevisiae Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
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
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 G 171 Saccharomyces cerevisiae Gene Name(s): RPB7 YDR404C D9509.22
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 H 146 Saccharomyces cerevisiae Gene Name(s): RPB8 YOR224C YOR50-14
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 I 122 Saccharomyces cerevisiae Gene Name(s): RPB9 YGL070C
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 J 70 Saccharomyces cerevisiae Gene Name(s): RPB10 YOR210W
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 K 120 Saccharomyces cerevisiae Gene Name(s): RPB11 YOL005C
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 L 70 Saccharomyces cerevisiae Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
TRANSCRIPTION FACTOR BYE1 X 146 Saccharomyces cerevisiae Fragment: RESIDUES 225-370
Gene Name(s): BYE1 YKL005C YKL150
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3' N 14 Synthetic construct
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' P 11 Synthetic construct
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' T 26 Synthetic construct

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: 3.6 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.175
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 222.24 α = 90.00
b = 391.58 β = 90.00
c = 281.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-07-17
  • Released Date: 2013-09-11
  • Deposition author(s): Kinkelin, K., Wozniak, G.G., Rothbart, S.B., Lidschreiber, M., Strahl, B.D., Cramer, P.

Revision History

  • 2013-10-02
    Type: Citation | Details: JRNL