8TMV

HTLV-1 capsid protein N-terminal domain triclinic crystal form with phosphate ion

PDB DOI: https://doi.org/10.2210/pdb8TMV/pdb

Classification: VIRAL PROTEIN
Organism(s): HTLV-1 subtype C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-07-31 Released: 2024-08-07
Deposition Author(s): Yu, R.J., Li, N., Jacques, D.A.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.230
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

HTLV-1 capsid protein N-terminal domain triclinic crystal form with phosphate ion

Yu, R.J., Li, N., Jacques, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 14.24 kDa
Atom Count: 1,049
Modelled Residue Count: 125
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein p24	A	127	HTLV-1 subtype C	Mutation(s): 0
UniProt
Find proteins for U3RC00 (Human T-cell leukemia virus type I) Explore U3RC00 Go to UniProtKB: U3RC00
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U3RC00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.230
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.195	α = 65.19
b = 30.72	β = 79.3
c = 36.081	γ = 89.56

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	214344/Z/18/Z

Revision History (Full details and data files)

Version 1.0: 2024-08-07
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 R01GM157729.