3RG5

Crystal Structure of Mouse tRNA(Sec)

PDB DOI: https://doi.org/10.2210/pdb3RG5/pdb
NAKB: 3RG5

Classification: RNA
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2011-04-07 Released: 2011-06-08
Deposition Author(s): Wahl, M.C., Ganichkin, O.M., Anedchenko, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.253
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

Ganichkin, O.M., Anedchenko, E.A., Wahl, M.C.

(2011) PLoS One 6: e20032-e20032

PubMed: 21629646 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0020032
Primary Citation of Related Structures:
3RG5

PubMed Abstract:
Selenocysteine tRNAs (tRNA(Sec)) exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec)-interacting factors are incompletely understood.

Organizational Affiliation

Abteilung Strukturbiochemie, Freie Universität Berlin, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 55.74 kDa
Atom Count: 3,887
Modelled Residue Count: 172
Deposited Residue Count: 172
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA(Sec)	A, B	86	Mus musculus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.253
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.872	α = 90
b = 96.055	β = 105.06
c = 71.841	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Wahl, M.C.

Ganichkin, O.M.

Anedchenko, E.A.

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-11
Changes: Database references
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description

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