[English] 日本語
Yorodumi
- PDB-1jtf: Crystal Structure Analysis of VP39-F180W mutant and m7GpppG complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jtf
TitleCrystal Structure Analysis of VP39-F180W mutant and m7GpppG complex
ComponentsVP39
KeywordsTRANSFERASE / VP39 / mRNA Cap-binding protein / methyltransferase / mutant
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / methylation / RNA binding
Similarity search - Function
mRNA methyltransferase-like / Poxvirus/kinetoplastid-type cap-specific nucleoside 2-O-methyltransferase / Poxvirus cap-specific nucleoside 2-O-methyltransferase / Poly A polymerase regulatory subunit / Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsHu, G. / Oguro, A. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Biochemistry / Year: 2002
Title: The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap.
Authors: Hu, G. / Oguro, A. / Li, C. / Gershon, P.D. / Quiocho, F.A.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8033
Polymers35,9601
Non-polymers8432
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.245, 67.741, 79.635
Angle α, β, γ (deg.)90.00, 118.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein VP39 / POLY(A) POLYMERASE REGULATORY SUBUNIT


Mass: 35960.473 Da / Num. of mol.: 1 / Fragment: residues 1-307 / Mutation: F180W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Plasmid: pPG177 / Production host: Escherichia coli (E. coli)
References: UniProt: P07617, polynucleotide adenylyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / m7GpppG


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, sodium citrate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Details: Hodel, A.E., (1996) Cell(Cambridge,Mass.), 85, 247.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG800011
20.125 M11AmSO4
30.1 Mcitrate11

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: CCD / Date: May 13, 1999
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 22968 / Num. obs: 21940 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.61→2.74 Å / % possible all: 50
Reflection
*PLUS
Rmerge(I) obs: 0.107

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SAINT(SIEMENS)data reduction
SAINT(SIEMENS)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1217 9.998 %random
Rwork0.258 ---
all0.273 13007 --
obs0.273 12172 --
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 54 53 2512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg1.96
X-RAY DIFFRACTIONx_dihedral_angle_d24.46
X-RAY DIFFRACTIONx_improper_angle_d1.81
LS refinement shellResolution: 2.61→2.74 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.3 140 -
Rwork0.27 --
obs-1397 50 %
Refinement
*PLUS
Rfactor obs: 0.273 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.3 / Rfactor Rwork: 0.27

+
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