[English] 日本語
Yorodumi
- PDB-5cd1: Structure of an asymmetric tetramer of human tRNA m1A58 methyltra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cd1
TitleStructure of an asymmetric tetramer of human tRNA m1A58 methyltransferase in a complex with SAH and tRNA3Lys
Components
  • tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
  • tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
  • tRNA3Lys
KeywordsTRANSFERASE/RNA / class I methyltransferase fold / tRNA modification / SAM-dependent methyl transfer / TRANSFERASE-RNA complex
Function / homology
Function and homology information


mRNA (adenine-N1-)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA modification in the nucleus and cytosol / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA processing / RNA binding / nucleoplasm / nucleus
Similarity search - Function
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / Gcd10p family / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / Gcd10p family / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / RNA / RNA (> 10) / tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A / tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFiner-Moore, J. / Czudnochowski, N. / O'Connell III, J.D. / Wang, A.L. / Stroud, R.M.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51232 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM0082250 United States
German Research Foundation (DFG)CZ 205/1-1 Germany
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.
Authors: Finer-Moore, J. / Czudnochowski, N. / O'Connell, J.D. / Wang, A.L. / Stroud, R.M.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
B: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
D: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A
E: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
M: tRNA3Lys
N: tRNA3Lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,00810
Polymers224,1936
Non-polymers8154
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27790 Å2
ΔGint-181 kcal/mol
Surface area67720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.240, 137.440, 157.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A / tRNA(m1A58)-methyltransferase subunit TRMT61A / tRNA(m1A58)MTase subunit TRMT61A


Mass: 31420.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT61A, C14orf172, TRM61 / Plasmid: pET17b-6HisTrm6-Trm61
Details (production host): 3C protease cleavage site added C-terminal to the 6His tag
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FX7, tRNA (adenine58-N1)-methyltransferase
#2: Protein tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 / tRNA(m1A58)-methyltransferase subunit TRM6 / tRNA(m1A58)MTase subunit TRM6


Mass: 55883.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT6, KIAA1153, TRM6, CGI-09 / Plasmid: pET17b-6HisTrm6-Trm61
Details (production host): 3C protease cleavage site added C-terminal to 6His tag
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJA5
#3: RNA chain tRNA3Lys


Mass: 24792.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 339572
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAH, 1mM MgCl2 and 50mM Hepes pH7.5) mixed with 1 microliter reservoir solution (0.1M NaAcetate, pH4.8-5.0,2% ...Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAH, 1mM MgCl2 and 50mM Hepes pH7.5) mixed with 1 microliter reservoir solution (0.1M NaAcetate, pH4.8-5.0,2% w/v PEG 4000, and 15% v/v MPD) over 1000 microliter reservoir solution
PH range: 4.8-5.0

-
Data collection

DiffractionMean temperature: 103.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014
RadiationMonochromator: double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.6→102.3 Å / Num. obs: 32882 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.308 / Net I/σ(I): 6.4
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.87 / Mean I/σ(I) obs: 1 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CCB

5ccb


Resolution: 3.6→59.392 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 1636 5 %Random selection
Rwork0.2316 31075 --
obs0.2337 32711 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→59.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9637 3200 54 0 12891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413480
X-RAY DIFFRACTIONf_angle_d0.76318994
X-RAY DIFFRACTIONf_dihedral_angle_d14.0495387
X-RAY DIFFRACTIONf_chiral_restr0.042256
X-RAY DIFFRACTIONf_plane_restr0.0031875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70590.45911270.41312458X-RAY DIFFRACTION96
3.7059-3.82550.35491300.34882568X-RAY DIFFRACTION100
3.8255-3.96220.35211470.30242546X-RAY DIFFRACTION100
3.9622-4.12080.33111280.28392568X-RAY DIFFRACTION100
4.1208-4.30830.30921230.25122592X-RAY DIFFRACTION100
4.3083-4.53530.2781380.22392580X-RAY DIFFRACTION100
4.5353-4.81940.25991460.20652576X-RAY DIFFRACTION100
4.8194-5.19130.28361330.21592584X-RAY DIFFRACTION100
5.1913-5.71330.2621390.21912609X-RAY DIFFRACTION100
5.7133-6.53910.28811370.22932627X-RAY DIFFRACTION100
6.5391-8.23510.24631430.19582627X-RAY DIFFRACTION99
8.2351-59.40010.1911450.17892740X-RAY DIFFRACTION98

+
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