5XOG

RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 5XOG

Classification: TRANSCRIPTION

Total Structure Weight: 556716.63


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase subunit A 1743 Komagataella phaffii EC#: 2.7.7.6 IUBMB
Gene Name(s): PAS_chr3_0568
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta B 1227 Komagataella phaffii EC#: 2.7.7.6 IUBMB
Gene Name(s): PAS_chr2-1_0125
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase II third largest subunit B44, part of central core C 304 Komagataella phaffii Gene Name(s): PAS_chr4_0344
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase II subunit B32 D 186 Komagataella phaffii Gene Name(s): PAS_chr2-2_0104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III E 214 Komagataella phaffii Gene Name(s): PAS_chr3_0157
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III F 155 Komagataella phaffii Gene Name(s): PAS_chr2-2_0434
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase II subunit G 171 Komagataella phaffii Gene Name(s): PAS_chr4_0906
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III H 145 Komagataella phaffii Gene Name(s): PAS_chr2-2_0309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit I 115 Komagataella phaffii Gene Name(s): RPB9 PP7435_Chr1-1144
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III J 72 Komagataella phaffii Gene Name(s): PAS_chr2-1_0223
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase II subunit B12.5 K 118 Komagataella phaffii Gene Name(s): PAS_chr3_0244
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase subunit ABC10-alpha L 72 Komagataella phaffii Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Transcription elongation factor 1 homolog M 85 Komagataella pastoris Fragment: UNP residues 1-82
Mutation: N53G, L54Q, S55R
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Spt4/5 complex component W 83 Komagataella phaffii Fragment: UNP residues 736-815
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') P 17 Synthetic construct
DNA (39-MER) T 39 Synthetic construct
DNA (30-MER) N 30 Synthetic construct

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.195
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 155.25 α = 90.00
b = 159.91 β = 90.00
c = 268.93 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-05-28
  • Released Date: 2017-08-16
  • Deposition author(s): Ehara, H., Shirouzu, M., Sekine, S.

Revision History

  • 2017-08-23
    Type: Database references
  • 2017-09-13
    Type: Database references