4X8W | pdb_00004x8w

dsRBD3 of Loquacious

PDB DOI: https://doi.org/10.2210/pdb4X8W/pdb

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

Deposited: 2014-12-10 Released: 2016-01-13
Deposition Author(s): Jakob, L., Treiber, N., Treiber, T., Stotz, M., Meister, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.251 (Depositor), 0.260 (DCC)
R-Value Work:
0.206 (Depositor), 0.220 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the dsRBD3 of Loquacious reveals features for dimerization and Dicer1-interaction

Jakob, L., Treiber, T., Treiber, N., Stotz, M., Meister, G.

To be published.

Macromolecule Content

Total Structure Weight: 60.75 kDa
Atom Count: 3,699
Modeled Residue Count: 491
Deposited Residue Count: 573
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Loquacious, isoform B	A, B, C, D, E A, B, C, D, E, F, G	75	Drosophila melanogaster	Mutation(s): 0 Gene Names: loqs, CG6866, Dmel_CG6866
UniProt
Find proteins for Q9VJY9 (Drosophila melanogaster) Explore Q9VJY9 Go to UniProtKB: Q9VJY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9VJY9
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Loquacious	H	48	Drosophila melanogaster	Mutation(s): 0 Gene Names: Loquacious
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C, D, E A, B, C, D, E, F, G	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.251 (Depositor), 0.260 (DCC)
R-Value Work: 0.206 (Depositor), 0.220 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.018	α = 90
b = 112.97	β = 90
c = 114.049	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
SHARP	phasing
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, 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.