3BNQ | pdb_00003bnq

Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the Presence of SrCl2 (A1555G mutant, Br-derivative)

PDB DOI: https://doi.org/10.2210/pdb3BNQ/pdb
NAKB: 3BNQ

Classification: RNA
Mutation(s): No

Deposited: 2007-12-14 Released: 2008-06-24
Deposition Author(s): Kondo, J., Westhof, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.269 (Depositor), 0.250 (DCC)
R-Value Work:
0.229 (Depositor), 0.224 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates

Kondo, J., Westhof, E.

(2008) Nucleic Acids Res 36: 2654-2666

PubMed: 18346970 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkn112
Primary Citation Related Structures:
3BNL, 3BNN, 3BNO, 3BNP, 3BNQ, 3BNR, 3BNS, 3BNT

PubMed Abstract:
The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or bacteria have been solved. The resting 'off' state of the mitochondrial wild-type A site is surprisingly different from that of the bacterial A site. The mitochondrial A1555G mutant has two types of the 'off' states; one is similar to the mitochondrial wild-type 'off' state and the other is similar to the bacterial 'off' state. Our present results indicate that the dynamics of the A site in bacteria and mitochondria are different, a property probably related to the small number of tRNAs used for decoding in mitochondria. Based on these structures, we propose a hypothesis for the molecular mechanism of non-syndromic hearing loss due to the mitochondrial A1555G mutation.

Organizational Affiliation

Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084 Strasbourg, France.

Macromolecule Content

Total Structure Weight: 30.36 kDa
Atom Count: 2,097
Modeled Residue Count: 90
Deposited Residue Count: 90
Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
A site of human mitochondrial ribosome, A chain	A, B, C	23	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
A site of human mitochondrial ribosome, B chain	D	21	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAR Query on PAR Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	PAROMOMYCIN C₂₃ H₄₅ N₅ O₁₄ UOZODPSAJZTQNH-LSWIJEOBSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
SR Query on SR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B]	E [auth A] G [auth B] H [auth B] J [auth C] K [auth C] E [auth A], G [auth B], H [auth B], J [auth C], K [auth C], L [auth C], N [auth D], O [auth D]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth C]	F [auth A], M [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.269 (Depositor), 0.250 (DCC)
R-Value Work: 0.229 (Depositor), 0.224 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.266	α = 90
b = 76.056	β = 117.06
c = 55.912	γ = 90

Software Package:

Software Name	Purpose
SCALA	data processing
SOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-06-24

Deposition Author(s):

Kondo, J.

Westhof, E.

Revision History (Full details and data files)

Version 1.0: 2008-06-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Structure summary