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- PDB-5cky: Crystal Structure of the MTERF1 R162A substitution bound to the t... -

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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) / Mitochondrial transcription termination factor 1 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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