9O0D | pdb_00009o0d

crystal structure of rSAMD9 tRNase domain

PDB DOI: https://doi.org/10.2210/pdb9O0D/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Oryctolagus cuniculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-02 Released: 2025-07-02
Deposition Author(s): Deng, J.P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.277 (Depositor), 0.284 (DCC)
R-Value Work:
0.228 (Depositor), 0.244 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural and Functional Studies of Rabbit SAMD9 Reveal a Distinct tRNase Module That Underlies the Antiviral Activity

Chaturvedi, J., Zhang, F., Zhang, C., Badhe, S., Xiang, Y., Deng, J.

To be published.

Macromolecule Content

Total Structure Weight: 108.71 kDa
Atom Count: 7,064
Modeled Residue Count: 862
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rSAMD9	A, B, C, D	234	Oryctolagus cuniculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.277 (Depositor), 0.284 (DCC)
R-Value Work: 0.228 (Depositor), 0.244 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.984	α = 90
b = 142.486	β = 90
c = 83.133	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI151638

Revision History (Full details and data files)

Version 1.0: 2025-07-02
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.