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- PDB-5co0: Crystal Structure of the MTERF1 Y288A substitution bound to the t... -

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Basic information

Entry
Database: PDB / ID: 5co0
TitleCrystal Structure of the MTERF1 Y288A 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) / Transcription termination factor 1, mitochondrial / Transcription termination factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 18, 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6624
Polymers50,6233
Non-polymers391
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-44 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.537, 90.440, 160.514
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: 37119.086 Da / Num. of mol.: 1 / Mutation: Y288A
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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium Acetate, 01.M Tris HCl pH 8.0, 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 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.54→80.26 Å / Num. obs: 21454 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.023 / Net I/σ(I): 26.3 / Num. measured all: 155685
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.54-2.847.40.71234437360130.8530.281100
5.68-80.266.80.01973.413879203610.00899.4

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVA

3mva


Resolution: 2.65→80.26 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.368 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.53 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 972 5.1 %RANDOM
Rwork0.2062 ---
obs0.2091 17909 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.36 Å2 / Biso mean: 59.248 Å2 / Biso min: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 2.65→80.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 896 1 24 3510
Biso mean--116.29 47.63 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0173630
X-RAY DIFFRACTIONr_bond_other_d0.0010.023142
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.7375083
X-RAY DIFFRACTIONr_angle_other_deg1.0137257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57924.087115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74115520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1351521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02804
LS refinement shellResolution: 2.65→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 58 -
Rwork0.358 1312 -
all-1370 -
obs--100 %

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