7K07 | pdb_00007k07

Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3-prime - 5-prime exoribonucleases

• PDB DOI: https://doi.org/10.2210/pdb7K07/pdb

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


• Deposited: 2020-09-03 Released: 2021-10-06 
• Deposition Author(s): Thapar, R., Arvai, A.S., Tainer, J.A.
• Funding Organization(s): Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3'- 5' exoribonucleases

Thapar, R., Arvai, A.S., Tainer, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.05 kDa 
• Atom Count: 3,435 
• Modelled Residue Count: 400 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERI1 exoribonuclease 3	A, B	216	Homo sapiens	Mutation(s): 0  Gene Names: ERI3, PINT1, PRNPIP, PRNPIP1 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43414 (Homo sapiens) Explore O43414  Go to UniProtKB:  O43414
PHAROS:  O43414 GTEx:  ENSG00000117419

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	C [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MN	D [auth A], E [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.627	α = 90
b = 74.777	β = 90
c = 96.725	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Thapar, R., Arvai, A.S., Tainer, J.A.

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Funding Organization	Location	Grant Number
Robert A. Welch Foundation		--

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary