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- PDB-3mva: Crystal structure of human MTERF1 bound to the termination sequence -

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Basic information

Entry
Database: PDB / ID: 3mva
TitleCrystal structure of human MTERF1 bound to the termination sequence
Components
  • 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')
  • 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, mitochondrial
KeywordsTRANSCRIPTION/DNA / all alpha-helix / protein-DNA / transcription factor / termination / mitochondria / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsYakubovskaya, E. / Mejia, E. / Byrnes, J. / Hambardjieva, E. / Garcia-Diaz, M.
CitationJournal: Cell(Cambridge,Mass.) / 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
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Transcription termination factor, 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)52,8283
Polymers52,8283
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-41 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.631, 89.709, 161.293
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, mitochondrial / Mitochondrial transcription termination factor 1 / mTERF


Mass: 39324.582 Da / Num. of mol.: 1 / Fragment: residues 57-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTERF, MTERF1 / Plasmid: pTEV-HMPB3 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic (DE3) / References: UniProt: Q99551
#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
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.09, 0.9195, 0.9197, 0.9000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.091
20.91951
30.91971
40.91
ReflectionResolution: 2.2→50 Å / Num. obs: 32806 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Χ2: 1.46 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.246.50.60216080.83699.1
2.24-2.286.90.5316290.82599.9
2.28-2.327.20.45816270.865100
2.32-2.377.30.36916310.849100
2.37-2.427.30.29116460.922100
2.42-2.487.40.24116090.917100
2.48-2.547.30.1916530.948100
2.54-2.617.40.15916341.01100
2.61-2.697.40.12916231.025100
2.69-2.777.40.10516481.1100
2.77-2.877.40.08716431.139100
2.87-2.997.40.07116591.297100
2.99-3.127.40.0616291.39999.9
3.12-3.297.30.04516511.58299.9
3.29-3.497.30.04416561.819100
3.49-3.767.30.04416692.159100
3.76-4.147.10.04516552.76399.8
4.14-4.7470.04416753.03499.6
4.74-5.976.80.03916932.42899.8
5.97-506.50.03615682.42787.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.987 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.795 / SU ML: 1.84 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 2414 7.67 %
Rwork0.205 --
obs0.208 31467 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.872 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 266.09 Å2 / Biso mean: 66.465 Å2 / Biso min: 34.32 Å2
Baniso -1Baniso -2Baniso -3
1-7.539 Å2-0 Å2-0 Å2
2---14.028 Å2-0 Å2
3----1.138 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 896 0 118 3617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063650
X-RAY DIFFRACTIONf_angle_d1.2435111
X-RAY DIFFRACTIONf_chiral_restr0.097590
X-RAY DIFFRACTIONf_plane_restr0.004495
X-RAY DIFFRACTIONf_dihedral_angle_d21.0761449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2440.3061140.2581496161083
2.244-2.2920.2651130.251524163787
2.292-2.3460.3081180.2391648176690
2.346-2.4040.3121280.2331629175792
2.404-2.4690.2751540.2291645179994
2.469-2.5420.2791400.2291718185896
2.542-2.6240.2831470.2211720186796
2.624-2.7180.2711410.221724186597
2.718-2.8260.291490.2371734188398
2.826-2.9550.2881450.2441753189898
2.955-3.1110.3091510.2491764191599
3.111-3.3050.2281540.2041773192799
3.305-3.560.2511520.20617841936100
3.56-3.9180.251480.18718031951100
3.918-4.4830.2011580.1621801195999
4.483-5.6420.1821550.1551820197599
5.642-29.990.2161470.1861717186490
Refinement TLS params.Method: refined / Origin x: -19.1661 Å / Origin y: 11.4447 Å / Origin z: -18.4619 Å
111213212223313233
T0.3275 Å20.1493 Å2-0.0333 Å2-0.4323 Å2-0.0556 Å2--0.3082 Å2
L0.5251 °20.4369 °2-0.1014 °2-1.0656 °2-0.5525 °2--1.0359 °2
S-0.0503 Å °0.0562 Å °0.0439 Å °0.0216 Å °0.0443 Å °-0.183 Å °-0.1122 Å °-0.0496 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allO73 - 396
2X-RAY DIFFRACTION1allD1 - 22
3X-RAY DIFFRACTION1allE1 - 22
4X-RAY DIFFRACTION1allO1 - 450

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