4EXT | pdb_00004ext

Structure of polymerase-interacting domain of human Rev1 in complex with translesional synthesis polymerase zeta

• PDB DOI: https://doi.org/10.2210/pdb4EXT/pdb

• Classification: TRANSFERASE/TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-01 Released: 2013-05-08 
• Deposition Author(s): Liu, D.N., Ryu, K.S., Ko, J.S., Choi, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.285 (Depositor) 
• R-Value Work: 
  0.224 (Depositor), 0.240 (DCC) 

Literature

Insights into the scaffold mechanism of human Rev1 in translesional synthesis revealed by structural studies on its polymerase-interacting domain

Liu, D.N., Ryu, K.S., Ko, J.S., Choi, B.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.33 kDa 
• Atom Count: 2,685 
• Modeled Residue Count: 317 
• Deposited Residue Count: 323 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein REV1	A	96	Homo sapiens	Mutation(s): 0  Gene Names: REV1, REV1L EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBZ9 (Homo sapiens) Explore Q9UBZ9  Go to UniProtKB:  Q9UBZ9
PHAROS:  Q9UBZ9 GTEx:  ENSG00000135945

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from DNA polymerase zeta catalytic subunit	B	23	Homo sapiens	Mutation(s): 0  Gene Names: REV3L, POLZ, REV3 EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for O60673 (Homo sapiens) Explore O60673  Go to UniProtKB:  O60673
PHAROS:  O60673 GTEx:  ENSG00000009413

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitotic spindle assembly checkpoint protein MAD2B	C	204	Homo sapiens	Mutation(s): 0  Gene Names: MAD2L2, MAD2B, REV7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI95 (Homo sapiens) Explore Q9UI95  Go to UniProtKB:  Q9UI95
PHAROS:  Q9UI95 GTEx:  ENSG00000116670

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.285 (Depositor) 
• R-Value Work:  0.224 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.699	α = 90
b = 71.523	β = 90
c = 84.053	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Liu, D.N., Ryu, K.S., Ko, J.S., Choi, B.S.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references