[English] 日本語
Yorodumi
- PDB-5cky: Crystal Structure of the MTERF1 R162A substitution bound to the t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cky
TitleCrystal Structure of the MTERF1 R162A substitution bound to the termination sequence.
Components
  • 5' -D (*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)-3'
  • 5'-D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)-3'
  • Transcription termination factor 1, mitochondrial
KeywordsTRANSCRIPTION/DNA / Protein-DNA / Transcription Factor / Mitochondria / Termination / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


termination of mitochondrial transcription / Mitochondrial transcription termination / DNA geometric change / mitochondrial nucleoid / DNA-templated transcription termination / Transcriptional activation of mitochondrial biogenesis / double-stranded DNA binding / nucleic acid binding / mitochondrial matrix / regulation of DNA-templated transcription ...termination of mitochondrial transcription / Mitochondrial transcription termination / DNA geometric change / mitochondrial nucleoid / DNA-templated transcription termination / Transcriptional activation of mitochondrial biogenesis / double-stranded DNA binding / nucleic acid binding / mitochondrial matrix / regulation of DNA-templated transcription / mitochondrion / RNA binding
Similarity search - Function
Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription termination factor 1, mitochondrial / Transcription termination factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
Model detailsR162A
AuthorsByrnes, J. / Hauser, K. / Norona, L. / Mejia, E. / Simmerling, C. / Garcia-Diaz, M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00-ES015421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM100021 United States
United Mitochondrial Disease FoundationUMDF to M.G.D United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM092714 United States
Citation
Journal: J.Mol.Biol. / Year: 2016
Title: Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion.
Authors: Byrnes, J. / Hauser, K. / Norona, L. / Mejia, E. / Simmerling, C. / Garcia-Diaz, M.
#1: Journal: Cell / Year: 2010
Title: Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription.
Authors: Yakubovskaya, E. / Mejia, E. / Byrnes, J. / Hambardjieva, E. / Garcia-Diaz, M.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Source and taxonomy
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 13, 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 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
O: Transcription termination factor 1, mitochondrial
D: 5'-D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)-3'
E: 5' -D (*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)50,6293
Polymers50,6293
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-42 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.217, 91.161, 159.103
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Transcription termination factor 1, mitochondrial / cDNA FLJ51270 / highly similar to Transcription termination factor / mitochondrial


Mass: 37125.066 Da / Num. of mol.: 1 / Fragment: UNP residues 57-396 / Mutation: R162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTERF1 / Plasmid: PTEV-HMBP3 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express DE3 / References: UniProt: B4DPR9, UniProt: Q99551*PLUS
#2: DNA chain 5'-D(*AP*TP*TP*AP*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*CP*AP*TP*CP*TP*TP*A)-3'


Mass: 6678.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5' -D (*TP*AP*AP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*GP*TP*AP*AP*T)-3'


Mass: 6825.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Sodium Acetate, 0.1M Tris HCl, 15.5% PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.615→79.55 Å / Num. obs: 19776 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.4
Reflection shellResolution: 2.615→2.624 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVA

3mva


Resolution: 2.62→79.55 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.867 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.49 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1011 5.1 %RANDOM
Rwork0.2142 ---
obs0.2164 18744 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.44 Å2 / Biso mean: 53.18 Å2 / Biso min: 27.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.62→79.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 896 0 8 3501
Biso mean---35.54 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0173640
X-RAY DIFFRACTIONr_bond_other_d0.0010.023143
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.7375097
X-RAY DIFFRACTIONr_angle_other_deg1.01637264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23624.224116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42415520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6191520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02807
X-RAY DIFFRACTIONr_mcbond_it3.8995.1161295
X-RAY DIFFRACTIONr_mcbond_other3.8965.1151294
X-RAY DIFFRACTIONr_mcangle_it5.8487.6751617
LS refinement shellResolution: 2.615→2.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 68 -
Rwork0.35 1376 -
all-1444 -
obs--100 %

+
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