7ULN | pdb_00007uln

Turnip yellows virus N-terminal readthrough domain

PDB DOI: https://doi.org/10.2210/pdb7ULN/pdb

Classification: VIRAL PROTEIN
Organism(s): Turnip yellows virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-05 Released: 2022-11-02
Deposition Author(s): Schiltz, C.J., Chappie, J.S.
Funding Organization(s): United States Department of Agriculture (USDA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.196 (Depositor), 0.192 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.175 (Depositor)

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

Literature

Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids

Schiltz, C.J., Wilson, J.R., Hosford, C.J., Adams, M.C., Preising, S.E., DeBlasio, S.L., MacLeod, H.J., Van Eck, J., Heck, M.L., Chappie, J.S.

(2022) Nat Commun 13: 6368

DOI: https://doi.org/10.1038/s41467-022-33979-2

Macromolecule Content

Total Structure Weight: 53.89 kDa
Atom Count: 4,409
Modeled Residue Count: 472
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein P3-RTD	A, B	238	Turnip yellows virus	Mutation(s): 0 Gene Names: ORF3/ORF5
UniProt
Find proteins for P09514 (Turnip yellows virus (isolate FL-1)) Explore P09514 Go to UniProtKB: P09514
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09514
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.196 (Depositor), 0.192 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.434	α = 90
b = 74.859	β = 90
c = 130.779	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-02

Deposition Author(s):

Funding Organization	Location	Grant Number
United States Department of Agriculture (USDA)	United States	2019-05200

Revision History (Full details and data files)

Version 1.0: 2022-11-02
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.