8VIV

Crystal structure of FBF-2 RBD in complex with gld-1 FBEa* RNA

PDB DOI: https://doi.org/10.2210/pdb8VIV/pdb
NAKB: 8VIV

Classification: RNA BINDING PROTEIN
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-05 Released: 2024-11-27
Deposition Author(s): Qiu, C., Hall, T.M.T.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.232
R-Value Work: 0.197
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A higher order complex of PUF and partner proteins regulates gld-1 expression in the C elegans germline

Qiu, C., Crittenden, S.L., Carrick, B.H., Dillard, L.B., Dandey, V.P., Viverette, E.G., Wine, R.N., Campbell, Z.T., Wickens, M., Borgnia, M.J., Kimble, J., Hall, T.M.T.

To be published.

Macromolecule Content

Total Structure Weight: 50.46 kDa
Atom Count: 3,505
Modelled Residue Count: 412
Deposited Residue Count: 424
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fem-3 mRNA-binding factor 2	A	413	Caenorhabditis elegans	Mutation(s): 0 Gene Names: fbf-2, F21H12.5
UniProt
Find proteins for Q09312 (Caenorhabditis elegans) Explore Q09312 Go to UniProtKB: Q09312
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09312
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(CPAPUPGPUPUPGPCPCPAP*U)-3')	B	11	Caenorhabditis elegans
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.232
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.569	α = 90
b = 98.569	β = 90
c = 107.14	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SERGUI	data collection
Coot	model building
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
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.