[English] 日本語
Yorodumi
- PDB-4dcg: VACCINIA METHYLTRANSFERASE VP39 MUTANT D182A COMPLEXED WITH M7G A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dcg
TitleVACCINIA METHYLTRANSFERASE VP39 MUTANT D182A COMPLEXED WITH M7G AND S-ADENOSYLHOMOCYSTEINE
ComponentsVP39
KeywordsMRNA PROCESSING / METHYLATED GUANOSINE / METHYLTRANSFERASE MUTANT D182A / RNA CAP ANALOG / POLY(A) POLYMERASE / VACCINIA / TRANSCRIPTION / COMPLEX (TRANSFERASE-RNA CAP ANALOG)
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / virion component / methylation / methyltransferase cap1 / methyltransferase cap1 activity / 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
7-METHYLGUANOSINE / S-ADENOSYL-L-HOMOCYSTEINE / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
AuthorsHu, G. / Hodel, A.E. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.
Authors: Hu, G. / Gershon, P.D. / Hodel, A.E. / Quiocho, F.A.
History
DepositionJul 13, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5603
Polymers35,8771
Non-polymers6832
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.334, 66.735, 79.392
Angle α, β, γ (deg.)90.00, 117.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 35877.426 Da / Num. of mol.: 1 / Mutation: D182A, C-TERMINAL DELETION OF 26 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: BL21 (DE3) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
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-MG7 / 7-METHYLGUANOSINE


Mass: 298.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 4.5 / Method: other
Details: used macroseeding, Hodel, A.E., (1996) Cell, 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: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: CCD / Date: Oct 28, 1997 / Details: GOBEL MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→20 Å / Num. obs: 31782 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 10 / Rsym value: 0.2 / % possible all: 92
Reflection
*PLUS
% possible obs: 91.8 % / Rmerge(I) obs: 0.051

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SMARTdata reduction
SAINTdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.8→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Cross valid method: FREE-R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 -10 %RANDOM
Rwork0.225 ---
obs0.225 31782 98 %-
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 47 0 2441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2

+
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