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), 0.255 (DCC)
R-Value Work:
0.202 (Depositor), 0.201 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F4JHB3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.255 (DCC)
R-Value Work: 0.202 (Depositor), 0.201 (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

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View more in-depth experimental data

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

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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.