7RVI | pdb_00007rvi

Segment from naked mole rat (elk T174S) prion protein 168-176 QYNNQNSFV

PDB DOI: https://doi.org/10.2210/pdb7RVI/pdb

Classification: PROTEIN FIBRIL
Organism(s): Heterocephalus glaber
Mutation(s): No

Deposited: 2021-08-18 Released: 2022-08-24
Deposition Author(s): Glynn, C., Rodriguez, J.A., Hernandez, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 1.05 Å
R-Value Free:
0.265 (Depositor), 0.256 (DCC)
R-Value Work:
0.222 (Depositor), 0.234 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural and Biophysical Consequences of Sequence Variation in the B2a2 Loop of Mammalian Prions

Glynn, C., Hernandez, E., Gallagher-Jones, M., Miao, J., Rodriguez, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 1.27 kDa
Atom Count: 88
Modeled Residue Count: 9
Deposited Residue Count: 9
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein	A	9	Heterocephalus glaber	Mutation(s): 0
UniProt
Find proteins for G5B4V6 (Heterocephalus glaber) Explore G5B4V6 Go to UniProtKB: G5B4V6
Entity Groups
UniProt Group	G5B4V6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC 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]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON CRYSTALLOGRAPHY
Resolution: 1.05 Å
R-Value Free: 0.265 (Depositor), 0.256 (DCC)
R-Value Work: 0.222 (Depositor), 0.234 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.76	α = 90
b = 4.85	β = 109.14
c = 21.52	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Rodriguez, J.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM128867
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1F31AI143368

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

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.