7U4A

Crystal Structure of Zika virus xrRNA1 mutant

PDB DOI: https://doi.org/10.2210/pdb7U4A/pdb
NAKB: 7U4A

Classification: RNA
Organism(s): Zika virus
Mutation(s): No

Deposited: 2022-02-28 Released: 2023-09-06
Deposition Author(s): Thompson, R.D., Carbaugh, D.L., Nielsen, J.R., Witt, C., Meganck, R.M., Rangadurai, A., Zhao, B., Bonin, J.P., Nathan, N.T., Marzluff, W.F., Frank, A.T., Lazear, H.M., Zhang, Q.
Funding Organization(s): University of North Carolina at Chapel Hill

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.270
R-Value Work: 0.214
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Dynamic Basis of Xrn1 Resistance in Mosquito-borne Flavivirus RNA

Thompson, R.D., Carbaugh, D.L., Nielsen, J.R., Witt, C., Meganck, R.M., Rangadurai, A., Zhao, B., Bonin, J.P., Nathan, N.T., Marzluff, W.F., Frank, A.T., Lazear, H.M., Zhang, Q.

To be published.

Macromolecule Content

Total Structure Weight: 23.35 kDa
Atom Count: 1,503
Modelled Residue Count: 70
Deposited Residue Count: 72
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (70-MER)	A	72	Zika virus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.270
R-Value Work: 0.214
R-Value Observed: 0.217
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.421	α = 90
b = 39.137	β = 94.339
c = 66.583	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-06

Deposition Author(s):

Funding Organization	Location	Grant Number
University of North Carolina at Chapel Hill	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-09-06
Type: Initial release

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 R01GM133198.