[English] 日本語
Yorodumi
- PDB-5x70: Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x70
TitleCrystal structure of Rice Dwarf Virus P5 in complex with a ssRNA oligomer
Components
  • RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')
  • mRNA capping enzyme P5
KeywordsTRANSFERASE/RNA / mRNA 5'-capping enzyme / guanylyltransferase / methyltransferase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


7-methylguanosine mRNA capping / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / host cell cytoplasm / GTP binding / RNA binding
Similarity search - Function
mRNA-capping enzyme P5, phytoreovirus
Similarity search - Domain/homology
RNA / Putative mRNA-capping enzyme P5
Similarity search - Component
Biological speciesRice dwarf virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNakamichi, Y. / Higashiura, A. / Nakagawa, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPSJP25251009 Japan
CitationJournal: To Be Published
Title: Crystal structure of capping enzyme from Rice dwarf virus
Authors: Nakamichi, Y. / Higashiura, A. / Narita, H. / Hagiwara, K. / Uehara-Ichiki, T. / Omura, T. / Nakagawa, A.
History
DepositionFeb 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA capping enzyme P5
C: mRNA capping enzyme P5
D: mRNA capping enzyme P5
B: mRNA capping enzyme P5
E: RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')
G: RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)367,0866
Polymers367,0866
Non-polymers00
Water00
1
A: mRNA capping enzyme P5
B: mRNA capping enzyme P5
E: RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')
G: RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)185,4814
Polymers185,4814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-41 kcal/mol
Surface area56830 Å2
MethodPISA
2
C: mRNA capping enzyme P5
D: mRNA capping enzyme P5


Theoretical massNumber of molelcules
Total (without water)181,6052
Polymers181,6052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-34 kcal/mol
Surface area58310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.754, 80.657, 145.734
Angle α, β, γ (deg.)104.74, 104.00, 95.29
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
mRNA capping enzyme P5


Mass: 90802.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rice dwarf virus (isolate O) / Strain: isolate O / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14583*PLUS, mRNA guanylyltransferase
#2: RNA chain RNA (5'-R(P*GP*GP*CP*AP*AP*A)-3')


Mass: 1938.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rice dwarf virus
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. N-TERMINAL GGS ARE EXPRESSION TAGS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350, 0.1M MES, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 50777 / % possible obs: 98.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.3
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2528 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X6X

5x6x


Resolution: 3.3→38.527 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 2669 5.29 %Random
Rwork0.2202 ---
obs0.2228 50417 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→38.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24149 109 0 0 24258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224838
X-RAY DIFFRACTIONf_angle_d0.40133708
X-RAY DIFFRACTIONf_dihedral_angle_d7.37114794
X-RAY DIFFRACTIONf_chiral_restr0.0413838
X-RAY DIFFRACTIONf_plane_restr0.0034182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.360.40091160.35412506X-RAY DIFFRACTION95
3.36-3.42460.38751010.30242463X-RAY DIFFRACTION98
3.4246-3.49440.34121600.27462536X-RAY DIFFRACTION98
3.4944-3.57040.32611580.27052417X-RAY DIFFRACTION98
3.5704-3.65340.31811350.25552566X-RAY DIFFRACTION99
3.6534-3.74460.36011370.25592502X-RAY DIFFRACTION99
3.7446-3.84580.30851400.24282537X-RAY DIFFRACTION98
3.8458-3.95890.28791180.24462482X-RAY DIFFRACTION99
3.9589-4.08650.26411460.23292557X-RAY DIFFRACTION99
4.0865-4.23240.27141090.21932558X-RAY DIFFRACTION99
4.2324-4.40160.23891580.20132456X-RAY DIFFRACTION99
4.4016-4.60160.25251630.19842527X-RAY DIFFRACTION99
4.6016-4.84380.27611300.1882533X-RAY DIFFRACTION99
4.8438-5.14660.24811540.19812512X-RAY DIFFRACTION99
5.1466-5.54290.21691880.20152482X-RAY DIFFRACTION99
5.5429-6.09880.23691160.21042578X-RAY DIFFRACTION99
6.0988-6.97670.30431540.22232509X-RAY DIFFRACTION99
6.9767-8.77280.21651560.19192517X-RAY DIFFRACTION99
8.7728-38.52990.23061300.18342510X-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://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