3LLH | pdb_00003llh

Crystal structure of the first dsRBD of TAR RNA-binding protein 2

PDB DOI: https://doi.org/10.2210/pdb3LLH/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-29 Released: 2010-12-08
Deposition Author(s): Yamashita, S., Kawazoe, M., Takemoto, C., Sekine, S., Wakiyama, M., Yokoyama, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.233 (Depositor), 0.236 (DCC)
R-Value Work:
0.185 (Depositor), 0.186 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

The structures of dsRBDs of human TRBP

Yamashita, S., Nagata, T., Kawazoe, M., Takemoto, C., Muto, Y., Sekine, S., Wakiyama, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 18.98 kDa
Atom Count: 1,023
Modeled Residue Count: 130
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RISC-loading complex subunit TARBP2	A, B	90	Homo sapiens	Mutation(s): 0 Gene Names: 6895
UniProt & NIH Common Fund Data Resources
Find proteins for Q15633 (Homo sapiens) Explore Q15633 Go to UniProtKB: Q15633
PHAROS: Q15633 GTEx: ENSG00000139546
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15633
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.233 (Depositor), 0.236 (DCC)
R-Value Work: 0.185 (Depositor), 0.186 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.184	α = 90
b = 51.184	β = 90
c = 42.828	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.