[English] 日本語
Yorodumi
- PDB-3bt7: Structure of E. coli 5-Methyluridine Methyltransferase TrmA in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bt7
TitleStructure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue
Components
  • RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')
  • tRNA (uracil-5-)-methyltransferase
KeywordsTRANSFERASE/RNA / methyluridine / methyltransferase / TrmA / RUMT / S-adenosyl-L-methionine / tRNA processing / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA folding / tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent / tRNA (uracil54-C5)-methyltransferase / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / rRNA binding / cytosol
Similarity search - Function
tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1070 / RNA methyltransferase TrmA, active site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / Vaccinia Virus protein VP39 ...tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1070 / RNA methyltransferase TrmA, active site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / Vaccinia Virus protein VP39 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA/tmRNA (uracil-C(5))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.43 Å
AuthorsAlian, A. / Stroud, R.M. / Finer-Moore, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases.
Authors: Alian, A. / Lee, T.T. / Griner, S.L. / Stroud, R.M. / Finer-Moore, J.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (uracil-5-)-methyltransferase
B: tRNA (uracil-5-)-methyltransferase
C: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')
D: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,6864
Polymers96,6864
Non-polymers00
Water4,702261
1
A: tRNA (uracil-5-)-methyltransferase
C: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)48,3432
Polymers48,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-17 kcal/mol
Surface area18310 Å2
MethodPISA
2
B: tRNA (uracil-5-)-methyltransferase
D: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)48,3432
Polymers48,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.407, 70.131, 107.950
Angle α, β, γ (deg.)90.00, 120.88, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASPASP1AA1 - 654 - 68
211METMETASPASP1BB1 - 654 - 68
321GLNGLNTHRTHR1AA67 - 6870 - 71
421GLNGLNTHRTHR1BB67 - 6870 - 71
531SERSERSERSER1AA7073
631SERSERSERSER1BB7073
741ILEILESERSER1AA72 - 8175 - 84
841ILEILESERSER1BB72 - 8175 - 84
951LEULEULEULEU1AA83 - 10186 - 104
1051LEULEULEULEU1BB83 - 10186 - 104
1161HISHISASPASP1AA103 - 233106 - 236
1261HISHISASPASP1BB103 - 233106 - 236
1371VALVALLYSLYS1AA235 - 366238 - 369
1471VALVALLYSLYS1BB235 - 366238 - 369
112GGCC4CC48 - 661 - 19
212GGCC4DD48 - 661 - 19

NCS ensembles :
ID
1
2

-
Components

#1: Protein tRNA (uracil-5-)-methyltransferase / tRNAM-5-U54 / methyltransferase / RUMT


Mass: 42298.137 Da / Num. of mol.: 2 / Mutation: E358Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trmA / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23003, tRNA (uracil54-C5)-methyltransferase
#2: RNA chain RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Mass: 6044.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM sodium cacodylate pH 7.4, 200 mM sodium sulfate, and 22 % PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2sodium cacodylate12
3sodium sulfate11
4sodium sulfate12
5PEG-800011
6PEG-800012

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.43→35.1 Å / Num. all: 90859 / Num. obs: 42023 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 5.7
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.7 / % possible all: 83.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SOLVEphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB entry 2BH2

2bh2


Resolution: 2.43→35.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.218 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28635 3230 7.7 %RANDOM
Rwork0.22509 ---
obs0.2297 38764 93.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.563 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 804 0 261 6979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226929
X-RAY DIFFRACTIONr_bond_other_d0.0020.024378
X-RAY DIFFRACTIONr_angle_refined_deg1.7812.1059568
X-RAY DIFFRACTIONr_angle_other_deg1.4343.00110684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58724.304309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.099151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1691546
X-RAY DIFFRACTIONr_chiral_restr0.0850.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217116
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.781.53692
X-RAY DIFFRACTIONr_mcbond_other0.1431.51470
X-RAY DIFFRACTIONr_mcangle_it1.45325963
X-RAY DIFFRACTIONr_scbond_it2.10233237
X-RAY DIFFRACTIONr_scangle_it3.3924.53605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 2 / Number: 531 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

TypeWeight position
medium positional0.5
medium thermal5
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 209 -
Rwork0.366 2533 -
obs--82.81 %

+
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