[English] 日本語
Yorodumi
- PDB-2o3v: Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o3v
TitleCrystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / aminoglycoside / antibiotics / ribosome / decoding site / Homo sapiens / Eukaryote / cytoplasmic / Translation inhibition / Stop codon readthrough
Function / homologyChem-N33 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKondo, J. / Hainrichson, M. / Nudelman, I. / Shallom-Shezifi, D. / Baasov, T. / Westhof, E.
CitationJournal: Chembiochem / Year: 2007
Title: Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites.
Authors: Kondo, J. / Hainrichson, M. / Nudelman, I. / Shallom-Shezifi, D. / Barbieri, C.M. / Pilch, D.S. / Westhof, E. / Baasov, T.
History
DepositionDec 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2253
Polymers14,7112
Non-polymers5151
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.620, 41.220, 56.910
Angle α, β, γ (deg.)90.000, 104.320, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: RNA chain RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')


Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-N33 / (2S,3R,4R,5S,6R)-3-AMINO-4-({[(2S,3R,4R,5S,6R)-3-AMINO-2-{[(1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL]OXY}METHOXY)-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2,5-DIOL


Mass: 514.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38N4O12
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6.5
Details: Sodium Cacodylate, Potassium chloride, 2-methyl-2,4-pentanediol, hexammine cobalt chloride, pH 6.5, VAPOR DIFFUSION, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2Potassium chloride11
32-methyl-2,4-pentanediol11
4hexammine cobalt chloride11
5Potassium chloride12
62-methyl-2,4-pentanediol12
7hexammine cobalt chloride12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 2.8→27.73 Å / Num. obs: 3225 / % possible obs: 99.3 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.06 / Χ2: 0.96 / Net I/σ(I): 11 / Scaling rejects: 85
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.8-2.93.590.3622.711443180.9100
2.9-3.023.550.2094.111013100.95100
3.02-3.153.60.137611863280.86100
3.15-3.323.570.1216.411353180.89100
3.32-3.533.580.0988.111913310.92100
3.53-3.83.520.0810.611173161.04100
3.8-4.183.480.0681311643340.8599.7
4.18-4.783.410.05915.811243260.9499.7
4.78-6.013.360.0520.110903201.14100
6.01-27.732.970.03726.410003241.193.6

-
Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→27.73 Å / FOM work R set: 0.66 / σ(F): 3
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
RfactorNum. reflection% reflection
Rfree0.29 286 8.8 %
Rwork0.232 --
obs-2995 92.1 %
Solvent computationBsol: 98.047 Å2
Displacement parametersBiso mean: 81.814 Å2
Baniso -1Baniso -2Baniso -3
1-8.345 Å20 Å23.312 Å2
2--3.709 Å20 Å2
3----12.054 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 918 35 41 994
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_d1.0312
X-RAY DIFFRACTIONc_improper_angle_d1.4
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.920.586430.605349392
2.92-3.070.284390.448329368
3.07-3.260.462380.298364402
3.26-3.50.392380.279366404
3.5-3.840.322420.249353395
3.84-4.350.281390.264354393
4.35-5.340.356340.258367401
5.34-100.442430.318376419
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION2nb22_xplor.paramnb22_xplor.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more