5MFX | pdb_00005mfx

Zika NS3 helicase:RNA complex

PDB DOI: https://doi.org/10.2210/pdb5MFX/pdb
NAKB: 5MFX

Classification: HYDROLASE
Organism(s): Zika virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-18 Released: 2017-01-11
Deposition Author(s): Jenkins, H.T., Ge, M., Chechik, M., Greive, S.J., Antson, A.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.191 (Depositor), 0.198 (DCC)
R-Value Work:
0.162 (Depositor), 0.173 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5MFX

This is version 1.1 of the entry. See complete history.

Literature

How Zika virus NS3 helicase grips the first nucleotide of the leading RNA strand

Jenkins, H.T., Ge, M., Chechik, M., Greive, S.J., Antson, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 53.81 kDa
Atom Count: 3,853
Modeled Residue Count: 439
Deposited Residue Count: 460
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	451	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A146CJH9 (Zika virus) Explore A0A146CJH9 Go to UniProtKB: A0A146CJH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A146CJH9
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R(PAPGPAPCP*U)-3')	B	9	Zika virus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.191 (Depositor), 0.198 (DCC)
R-Value Work: 0.162 (Depositor), 0.173 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.355	α = 90
b = 73.037	β = 93.97
c = 58.696	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data reduction
XDS	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT098230
Wellcome Trust	United Kingdom	WT101528

Revision History (Full details and data files)

Version 1.0: 2017-01-11
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.