[English] 日本語
Yorodumi
- PDB-4p5j: Crystal structure of the tRNA-like structure from Turnip Yellow M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p5j
TitleCrystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA
ComponentsTurnip yellow mosaic virus mRNA for the coat protein
KeywordsRNA / tRNA-mimic viral RNA Pseudoknot multifunctional
Function / homologyIRIDIUM HEXAMMINE ION / SPERMINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesTurnip yellow mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9912 Å
AuthorsColussi, T.M. / Costantino, D.A. / Hammond, J.A. / Ruehle, G.M. / Nix, J.C. / Kieft, J.S.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA046934 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM081346 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097333 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Citation
Journal: Nature / Year: 2014
Title: The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA.
Authors: Colussi, T.M. / Costantino, D.A. / Hammond, J.A. / Ruehle, G.M. / Nix, J.C. / Kieft, J.S.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA.
Authors: Hammond, J.A. / Rambo, R.P. / Kieft, J.S.
#2: Journal: Rna / Year: 2009
Title: Comparison and functional implications of the 3D architectures of viral tRNA-like structures.
Authors: Hammond, J.A. / Rambo, R.P. / Filbin, M.E. / Kieft, J.S.
History
DepositionMar 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Turnip yellow mosaic virus mRNA for the coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,37716
Polymers27,5931
Non-polymers3,78415
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-40 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.270, 101.570, 111.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

-
Components

#1: RNA chain Turnip yellow mosaic virus mRNA for the coat protein


Mass: 27593.316 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Turnip yellow mosaic virus / References: GenBank: 62226
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room ...Details: This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room temperature. After cooling, Spermidine was added to 0.5 mM. The reaction was centrifuged for 10 minutes at 13000 x g and then used in sitting-drop vapor diffusion crystallization at 4?C. 1 ?L of RNA solution was combined with 2 ?L of 10% MPD, 40 mM Na-Cacodylate pH 6.0, 12 mM Spermine, 80 mM NaCl, and 20 mM MgCl2. The well solution was 20-35% MPD. Crystals appeared and grew to full size over the course of 1-2 days.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0972 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 21, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 1.99→66 Å / Num. obs: 41343 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7.45 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.71
Reflection shellResolution: 1.99→2.03 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.19 / % possible all: 94.7

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9912→28.871 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 3790 9.17 %Random
Rwork0.2057 ---
obs0.2088 41334 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9912→28.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1785 100 126 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112078
X-RAY DIFFRACTIONf_angle_d1.7913295
X-RAY DIFFRACTIONf_dihedral_angle_d14.1481042
X-RAY DIFFRACTIONf_chiral_restr0.082420
X-RAY DIFFRACTIONf_plane_restr0.01384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9912-2.01640.32591260.30461239X-RAY DIFFRACTION90
2.0164-2.0430.39081390.29731395X-RAY DIFFRACTION100
2.043-2.07090.30241480.28831410X-RAY DIFFRACTION100
2.0709-2.10050.3231360.2831379X-RAY DIFFRACTION100
2.1005-2.13190.27851400.27461391X-RAY DIFFRACTION100
2.1319-2.16520.29821400.25671396X-RAY DIFFRACTION100
2.1652-2.20070.24961390.2361388X-RAY DIFFRACTION100
2.2007-2.23860.28121430.23461410X-RAY DIFFRACTION100
2.2386-2.27930.29251430.22771401X-RAY DIFFRACTION100
2.2793-2.32310.26411380.22621363X-RAY DIFFRACTION100
2.3231-2.37050.28251430.23161413X-RAY DIFFRACTION100
2.3705-2.4220.2771420.22791419X-RAY DIFFRACTION100
2.422-2.47830.24891410.22951377X-RAY DIFFRACTION100
2.4783-2.54030.33121430.25011396X-RAY DIFFRACTION100
2.5403-2.60890.27521420.24971396X-RAY DIFFRACTION100
2.6089-2.68560.29891430.25211404X-RAY DIFFRACTION100
2.6856-2.77220.2851470.25571400X-RAY DIFFRACTION100
2.7722-2.87120.29941420.27411395X-RAY DIFFRACTION100
2.8712-2.98610.37211330.23731391X-RAY DIFFRACTION100
2.9861-3.12180.21241430.20531404X-RAY DIFFRACTION100
3.1218-3.28620.24121360.18251403X-RAY DIFFRACTION100
3.2862-3.49180.23821410.18041413X-RAY DIFFRACTION100
3.4918-3.76080.18961390.17431369X-RAY DIFFRACTION100
3.7608-4.13830.2051430.17641421X-RAY DIFFRACTION100
4.1383-4.73490.17141440.16951387X-RAY DIFFRACTION100
4.7349-5.95680.20571380.15561392X-RAY DIFFRACTION100
5.9568-28.87360.20581380.20291392X-RAY DIFFRACTION98

+
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://pdbjlvh1.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