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- PDB-3n7q: Crystal structure of human mitochondrial mTERF fragment (aa 99-39... -

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Basic information

Entry
Database: PDB / ID: 3n7q
TitleCrystal structure of human mitochondrial mTERF fragment (aa 99-399) in complex with a 12-mer DNA encompassing the tRNALeu(UUR) binding sequence
Components
  • DNA (5'-D(*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*G)-3')
  • Transcription termination factor, mitochondrial
KeywordsTRANSCRIPTION / REPLICATION/DNA / Mitochondrial transcription termination factor-DNA complex / mitochondrial replication pausing-DNA complex / left-handed helical tandem repeat / Protein-DNA complex / REPLICATION-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
CITRIC ACID / DNA / DNA (> 10) / Transcription termination factor 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJimenez-Menendez, N. / Fernandez-Millan, P. / Rubio-Cosials, A. / Arnan, C. / Montoya, J. / Jacobs, H.T. / Bernado, P. / Coll, M. / Uson, I. / Sola, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat.
Authors: Jimenez-Menendez, N. / Fernandez-Millan, P. / Rubio-Cosials, A. / Arnan, C. / Montoya, J. / Jacobs, H.T. / Bernado, P. / Coll, M. / Uson, I. / Sola, M.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription termination factor, mitochondrial
B: DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*G)-3')
C: DNA (5'-D(*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2274
Polymers43,0353
Non-polymers1921
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.851, 99.851, 39.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Transcription termination factor, mitochondrial / Mitochondrial transcription termination factor 1 / mTERF


Mass: 35706.324 Da / Num. of mol.: 1 / Fragment: UNP residues 99-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTERF / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q99551
#2: DNA chain DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*CP*CP*GP*G)-3')


Mass: 3713.418 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*CP*GP*GP*GP*CP*TP*CP*TP*GP*CP*C)-3')


Mass: 3615.342 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorDetector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→31 Å / Num. all: 17262 / Num. obs: 17262
Reflection shellResolution: 2.4→2.55 Å / Num. unique all: 165

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Processing

Software
NameVersionClassification
EPMRphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SHELXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→31 Å / SU ML: 0.39 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 882 5.11 %
Rwork0.228 --
obs0.2306 17251 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.005 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9645 Å2-0 Å2-0 Å2
2--0.9645 Å2-0 Å2
3----1.9289 Å2
Refinement stepCycle: LAST / Resolution: 2.4→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 486 13 32 2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013018
X-RAY DIFFRACTIONf_angle_d1.3424177
X-RAY DIFFRACTIONf_dihedral_angle_d23.241172
X-RAY DIFFRACTIONf_chiral_restr0.077477
X-RAY DIFFRACTIONf_plane_restr0.005466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.55050.41691650.37672707X-RAY DIFFRACTION100
2.5505-2.74730.38611320.32692728X-RAY DIFFRACTION100
2.7473-3.02360.35461480.28592755X-RAY DIFFRACTION100
3.0236-3.46060.31291620.24192711X-RAY DIFFRACTION100
3.4606-4.35810.26921410.19592723X-RAY DIFFRACTION100
4.3581-310.20851340.19132745X-RAY DIFFRACTION100

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