8IGD | pdb_00008igd

The crystal structure of the minimal interaction domains of DRB7.2:DRB4 complex

PDB DOI: https://doi.org/10.2210/pdb8IGD/pdb

Classification: GENE REGULATION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-20 Released: 2024-06-26
Deposition Author(s): Paturi, S., Deshmukh, M.V.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.254 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The mechanism of DRB7.2:DRB4 mediated sequestering of endogenous inverted-repeat dsRNA precursors in plants

Paturi, S., Patra, D., Behera, P.C., Aute, R., Waghela, N., Kinatukara, P., Deshmukh, M.V.

(2025) Elife

DOI: https://doi.org/10.7554/elife.105762.1

Macromolecule Content

Total Structure Weight: 38.54 kDa
Atom Count: 2,080
Modeled Residue Count: 259
Deposited Residue Count: 336
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-binding domain (DsRBD)-containing protein	A, B	97	Arabidopsis thaliana	Mutation(s): 0 Gene Names: AT4G00420
UniProt
Find proteins for F4JHB3 (Arabidopsis thaliana) Explore F4JHB3 Go to UniProtKB: F4JHB3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F4JHB3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-binding protein 4	C, D	71	Arabidopsis thaliana	Mutation(s): 0 Gene Names: DBR4
UniProt
Find proteins for Q8H1D4 (Arabidopsis thaliana) Explore Q8H1D4 Go to UniProtKB: Q8H1D4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8H1D4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.254 (Depositor), 0.250 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.94	α = 90
b = 93.94	β = 90
c = 102.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	MLP0161

Revision History (Full details and data files)

Version 1.0: 2024-06-26
Type: Initial release
Version 1.1: 2025-06-18
Changes: Database references, Structure summary

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.