7N8W

Crystal structure of ERI2 nuclease bound to rAMP

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-06-15 Released: 2022-07-06 
  • Deposition Author(s): Thapar, R., Arvai, A.S., Tainer, J.A.
  • Funding Organization(s): Robert A. Welch Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI), Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of ERI2 nuclease bound to rAMP

Thapar, R., Arvai, A.S., Tainer, J.A.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ERI1 exoribonuclease 2
A, B
264Homo sapiensMutation(s): 0 
Gene Names: ERI2, EXOD1, KIAA1504
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for A8K979 (Homo sapiens)
Explore A8K979 
Go to UniProtKB:  A8K979
PHAROS:  A8K979
GTEx:  ENSG00000196678 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8K979
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP
Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B],
G [auth B],
H [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO
Download Ideal Coordinates CCD File 
I [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN
Download Ideal Coordinates CCD File 
E [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.832α = 90
b = 56.338β = 104.572
c = 75.852γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Robert A. Welch Foundation--
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA220430
Other privateUnited StatesGAP Award (to R.T., J.A.T)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM076660-04S1
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA092584

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description