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- PDB-5crk: Crystal Structure of the MTERF1 F243A substitution bound to the t... -

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Basic information

Entry
Database: PDB / ID: 5crk
TitleCrystal Structure of the MTERF1 F243A substitution bound to the termination sequence.
Components
  • DNA (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')
  • DNA (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')
  • 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 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 1.3Dec 18, 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

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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: DNA (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: DNA (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)50,6393
Polymers50,6393
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-37 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.743, 89.375, 159.910
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: 37135.086 Da / Num. of mol.: 1 / Fragment: UNP residues 53-376 / Mutation: F243A
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 DNA (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.) Homo sapiens (human)
#3: DNA chain DNA (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.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Sodium Acetate, 0.1M Tris HCl pH 8.0, 15% Peg 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→79.96 Å / Num. obs: 22892 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 34.1
Reflection shellResolution: 2.48→2.77 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVA

3mva


Resolution: 2.48→79.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.674 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1169 5.1 %RANDOM
Rwork0.2347 ---
obs0.2365 21690 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.62 Å2 / Biso mean: 68.473 Å2 / Biso min: 25.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20 Å2
2--0.09 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.48→79.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 896 0 1 3484
Biso mean---36.39 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0173629
X-RAY DIFFRACTIONr_bond_other_d0.0040.023140
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.7375082
X-RAY DIFFRACTIONr_angle_other_deg1.92637252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55923.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29315518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5071521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023425
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02804
X-RAY DIFFRACTIONr_mcbond_it5.9676.5041295
X-RAY DIFFRACTIONr_mcbond_other5.9486.5031294
X-RAY DIFFRACTIONr_mcangle_it8.3199.7671617
LS refinement shellResolution: 2.478→2.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 91 -
Rwork0.356 1585 -
all-1676 -
obs--100 %

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