[English] 日本語
Yorodumi
- PDB-3epp: Crystal structure of mRNA cap guanine-N7 methyltransferase (RNMT)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3epp
TitleCrystal structure of mRNA cap guanine-N7 methyltransferase (RNMT) in complex with sinefungin
ComponentsmRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / mRNA cap guanine-N7 methyltransferase / RNMT / sinefungin / Structural Genomics / Structural Genomics Consortium / SGC / mRNA capping / mRNA processing / Nucleus / Phosphoprotein / RNA-binding / S-adenosyl-L-methionine
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
SINEFUNGIN / mRNA cap guanine-N7 methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsAmaya, M.F. / Zeng, H. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. ...Amaya, M.F. / Zeng, H. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of mRNA cap guanine-N7 methyltransferase (RNMT) in complex with sinefungin.
Authors: Zeng, H. / Amaya, M.F. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mRNA cap guanine-N7 methyltransferase
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3094
Polymers73,5462
Non-polymers7632
Water2,972165
1
A: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1552
Polymers36,7731
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1552
Polymers36,7731
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.515, 73.650, 147.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7)-)-methyltransferase / RG7MT1 / mRNA cap methyltransferase / hcm1p / hCMT1 / hMet


Mass: 36773.211 Da / Num. of mol.: 2 / Fragment: Residues 165-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M KSCN, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 30, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 24532 / % possible obs: 97.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.094 / Χ2: 1.633 / Net I/σ(I): 15.874
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.494.60.3923811.89196
2.49-2.594.80.32823741.851196.2
2.59-2.74.80.27423901.778196.4
2.7-2.854.80.21124161.818196.7
2.85-3.024.90.15924121.857197.5
3.02-3.264.90.12424481.643197.6
3.26-3.584.90.08824891.504198.5
3.58-4.14.90.07224831.363198.2
4.1-5.174.90.06725201.316198.4
5.17-404.70.06726191.381196.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→38.92 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.68 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.501 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1260 5.1 %RANDOM
Rwork0.228 ---
obs0.231 24501 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.88 Å2 / Biso mean: 31.856 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å20 Å20 Å2
2--3.87 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.41→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 54 165 4411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224336
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9775839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92624.503191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68215744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3751515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023230
X-RAY DIFFRACTIONr_nbd_refined0.2150.21931
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5720.211
X-RAY DIFFRACTIONr_mcbond_it0.6541.52766
X-RAY DIFFRACTIONr_mcangle_it1.06724210
X-RAY DIFFRACTIONr_scbond_it1.82531876
X-RAY DIFFRACTIONr_scangle_it2.6214.51629
LS refinement shellResolution: 2.41→2.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 72 -
Rwork0.256 1610 -
all-1682 -
obs--91.76 %
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)
15.43240.6339-0.77051.3249-0.64911.6139-0.0168-0.28620.1354-0.0342-0.0146-0.0562-0.13850.05410.03140.1047-0.0566-0.0041-0.2342-0.0038-0.1213.5668.89735.293
21.35090.1484-0.7280.4428-0.32551.9430.0039-0.0452-0.0532-0.00410.05110.05760.0347-0.1159-0.0550.06660.0147-0.0169-0.2414-0.0102-0.1286-6.534-2.89835.239
33.8368-1.5446-1.62542.50320.17481.86970.08050.09830.1048-0.28380.0153-0.3835-0.0466-0.0233-0.09580.1186-0.01440.0169-0.2835-0.0156-0.154714.393-6.30117.138
41.27290.11190.38351.07360.57082.0099-0.11810.20310.111-0.0770.0996-0.0551-0.22310.12010.01850.11650.0010.0212-0.26570.0133-0.15157.1654.77824.938
51.2742-0.26480.62350.31130.37461.2972-0.09550.23940.02940.01570.0203-0.0372-0.04090.15330.07520.0558-0.0233-0.0059-0.13550.0304-0.08982.051-4.787-21.571
61.68510.51470.56741.15670.57321.6361-0.0436-0.16560.0623-0.01650.0664-0.0313-0.1725-0.0422-0.02270.0812-0.01470.0002-0.23250.011-0.1707-1.365-0.331-7.907
72.8855-0.2051-0.19570.8260.55942.5303-0.0144-0.02820.0495-0.06960.14490.0114-0.38240.2252-0.13050.048-0.02-0.0163-0.18480.0085-0.22082.534-0.0150.354
86.69641.6066-2.59211.1968-1.57542.124-0.0348-0.1759-0.50950.0368-0.1444-0.16040.10670.17140.17920.04390.0357-0.032-0.2521-0.0249-0.087416.136-6.637-11.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 36
2X-RAY DIFFRACTION2A37 - 151
3X-RAY DIFFRACTION3A152 - 190
4X-RAY DIFFRACTION4A191 - 313
5X-RAY DIFFRACTION5B5 - 83
6X-RAY DIFFRACTION6B88 - 183
7X-RAY DIFFRACTION7B184 - 231
8X-RAY DIFFRACTION8B232 - 313

+
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