[English] 日本語
Yorodumi
- PDB-5e9w: Crystal structure of mRNA cap guanine-N7 methyltransferase obtain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e9w
TitleCrystal structure of mRNA cap guanine-N7 methyltransferase obtained by limited proteolysis
ComponentsmRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / mRNA capping
Function / homology
Function and homology information


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 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 (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / 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-N7 methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.283 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 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jan 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
B: mRNA cap guanine-N7 methyltransferase
C: mRNA cap guanine-N7 methyltransferase
D: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,4028
Polymers146,8654
Non-polymers1,5384
Water5,531307
1
A: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.458, 99.157, 167.614
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 / RG7MT1 / mRNA (guanine-N(7)-)-methyltransferase / mRNA cap methyltransferase / hcm1p


Mass: 36716.160 Da / Num. of mol.: 4 / Fragment: UNP residues 165-476
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 / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES pH 6.5 and 25% PEG 4000, 1/5000 thermolysin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→29.58 Å / Num. obs: 57298 / % possible obs: 97 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.28→2.41 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.9 / % possible all: 97.6

-
Processing

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

3bgv


Resolution: 2.283→29.578 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2886 5.05 %
Rwork0.2201 --
obs0.2219 57204 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.283→29.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8989 0 104 307 9400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089297
X-RAY DIFFRACTIONf_angle_d1.34212468
X-RAY DIFFRACTIONf_dihedral_angle_d15.0343544
X-RAY DIFFRACTIONf_chiral_restr0.0571313
X-RAY DIFFRACTIONf_plane_restr0.0071574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2825-2.31990.32871300.27762549X-RAY DIFFRACTION97
2.3199-2.35990.31361470.25772589X-RAY DIFFRACTION98
2.3599-2.40280.33581530.25612548X-RAY DIFFRACTION97
2.4028-2.4490.28031420.24492531X-RAY DIFFRACTION97
2.449-2.4990.30521310.24682616X-RAY DIFFRACTION96
2.499-2.55330.31051440.24512535X-RAY DIFFRACTION97
2.5533-2.61260.29231010.24652631X-RAY DIFFRACTION97
2.6126-2.67790.28021230.2552596X-RAY DIFFRACTION96
2.6779-2.75030.27981420.23252560X-RAY DIFFRACTION97
2.7503-2.83120.24381380.23222580X-RAY DIFFRACTION97
2.8312-2.92250.27941240.23182588X-RAY DIFFRACTION97
2.9225-3.02680.25731560.23422537X-RAY DIFFRACTION96
3.0268-3.14790.27841440.2342596X-RAY DIFFRACTION97
3.1479-3.2910.24691340.22552615X-RAY DIFFRACTION97
3.291-3.46420.2291120.21722619X-RAY DIFFRACTION97
3.4642-3.68090.25051510.20432604X-RAY DIFFRACTION96
3.6809-3.96450.24991300.21272602X-RAY DIFFRACTION97
3.9645-4.36230.24211380.19172611X-RAY DIFFRACTION96
4.3623-4.99090.20031380.17722625X-RAY DIFFRACTION96
4.9909-6.27810.22451500.21122586X-RAY DIFFRACTION94
6.2781-29.58090.21161580.19092600X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 58.1387 Å / Origin y: 64.3557 Å / Origin z: 62.7484 Å
111213212223313233
T0.1216 Å20.011 Å20.0035 Å2-0.0897 Å20.0131 Å2--0.0726 Å2
L0.6064 °20.3329 °20.0389 °2-0.2266 °20.0408 °2--0.0451 °2
S0.0667 Å °-0.0306 Å °0.013 Å °0.0524 Å °-0.0459 Å °0.0152 Å °0.0296 Å °-0.0031 Å °-0.0196 Å °
Refinement TLS groupSelection details: all

+
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