[English] 日本語
Yorodumi
- PDB-5e9j: Crystal structure of the mRNA cap guanine-N7 methyltransferase - ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e9j
TitleCrystal structure of the mRNA cap guanine-N7 methyltransferase - modular lobe (416-456) deletion
ComponentsmRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / mRNA capping / RNA processing
Function / homology
Function and homology information


mRNA cap methyltransferase RNMT:RAMAC complex / mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...mRNA cap methyltransferase RNMT:RAMAC complex / mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / receptor complex / RNA binding / nucleoplasm / nucleus
Similarity search - Function
mRNA cap guanine-N7 methyltransferase, eukaryotes / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsPetit, P. / Cowling, V.H.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM.
Authors: Varshney, D. / Petit, A.P. / Bueren-Calabuig, J.A. / Jansen, C. / Fletcher, D.A. / Peggie, M. / Weidlich, S. / Scullion, P. / Pisliakov, A.V. / Cowling, V.H.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Feb 8, 2017Group: Data collection
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Jan 10, 2024Group: 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 cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
B: mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3254
Polymers64,5562
Non-polymers7692
Water00
1
A: mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6632
Polymers32,2781
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6632
Polymers32,2781
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.760, 114.380, 134.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase / RG7MT1 / mRNA (guanine-N(7)-)-methyltransferase / mRNA cap methyltransferase / hcm1p


Mass: 32278.158 Da / Num. of mol.: 2
Mutation: 416-456(GSGG),416-456(GSGG),416-456(GSGG),416-456(GSGG)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15 / Production host: Escherichia coli (E. coli)
References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1M Hepes pH 7.8, 15% isopropanol and 6% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3.47→87.21 Å / Num. obs: 13618 / % possible obs: 92.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.21 / Rsym value: 0.19 / Net I/σ(I): 6.6
Reflection shellResolution: 3.47→3.71 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.6 / % possible all: 67.6

-
Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BGV

3bgv


Resolution: 3.47→48.806 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 689 5.07 %
Rwork0.2365 --
obs0.238 13580 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.47→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 52 0 4510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034620
X-RAY DIFFRACTIONf_angle_d0.7846194
X-RAY DIFFRACTIONf_dihedral_angle_d15.061735
X-RAY DIFFRACTIONf_chiral_restr0.031644
X-RAY DIFFRACTIONf_plane_restr0.003787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4703-3.73810.4007820.33291909X-RAY DIFFRACTION69
3.7381-4.11410.34741470.29412587X-RAY DIFFRACTION95
4.1141-4.7090.31031430.23242734X-RAY DIFFRACTION99
4.709-5.93120.25751650.23362768X-RAY DIFFRACTION99
5.9312-48.81030.18851520.19422893X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3893-0.68580.53522.2218-1.18424.33-0.2088-0.04150.33990.1848-0.0503-0.1531-0.5673-0.1466-0.00010.7965-0.05220.02610.7352-0.0690.832692.8758133.89135.0849
23.22-0.0087-0.8023.39571.5763.80260.15960.2440.1438-0.2505-0.41410.7291-0.5662-0.6602-0.00030.8443-0.0115-0.05130.9439-0.07140.952970.8079124.6822101.6
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 3:276)
2X-RAY DIFFRACTION2(chain B and resseq 3:276)

+
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