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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.218 (Depositor), 0.219 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43414
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.218 (Depositor), 0.219 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.