7ULO | pdb_00007ulo

Potato leafroll virus N-terminal readthrough domain

PDB DOI: https://doi.org/10.2210/pdb7ULO/pdb

Classification: VIRAL PROTEIN
Organism(s): Potato leafroll virus
Expression System: Escherichia coli
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: 2.21 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.205 (Depositor)

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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: 50.75 kDa
Atom Count: 3,462
Modeled Residue Count: 428
Deposited Residue Count: 440
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein P3-RTD	A, B	209	Potato leafroll virus	Mutation(s): 0
UniProt
Find proteins for P17525 (Potato leafroll virus (strain Potato/Scotland/strain 1/1984)) Explore P17525 Go to UniProtKB: P17525
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17525
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein P3-RTD	C	22	Potato leafroll virus	Mutation(s): 0
UniProt
Find proteins for P17525 (Potato leafroll virus (strain Potato/Scotland/strain 1/1984)) Explore P17525 Go to UniProtKB: P17525
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17525
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.239 (Depositor), 0.240 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.229	α = 90
b = 65.147	β = 90
c = 109.681	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
SHELXDE	phasing

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: 2024-11-13
Changes: Data collection, Structure summary