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- PDB-3m66: Crystal structure of human Mitochondrial Transcription Terminatio... -

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Basic information

Entry
Database: PDB / ID: 3m66
TitleCrystal structure of human Mitochondrial Transcription Termination Factor 3
ComponentsmTERF domain-containing protein 1, mitochondrial
KeywordsTRANSCRIPTION / Mitochondrion / DNA binding protein / Transcription factor / Transcription termination / Transit peptide
Function / homology
Function and homology information


mitochondrial transcription / mitochondrial ribosome assembly / PINK1-PRKN Mediated Mitophagy / mitochondrial outer membrane / transcription cis-regulatory region binding / mitochondrial matrix / negative regulation of DNA-templated transcription / mitochondrion / cytosol
Similarity search - Function
Transcription termination factor 3, mitochondrial / Transcription termination factor 3, mitochondrial / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Transcription termination factor 3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSpahr, H. / Samuelsson, T. / Hallberg, B.M. / Gustafsson, C.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Structure of mitochondrial transcription termination factor 3 reveals a novel nucleic acid-binding domain.
Authors: Spahr, H. / Samuelsson, T. / Hallberg, B.M. / Gustafsson, C.M.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: mTERF domain-containing protein 1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,5631
Polymers31,5631
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.230, 32.240, 70.220
Angle α, β, γ (deg.)90.00, 106.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein mTERF domain-containing protein 1, mitochondrial / MTERF3


Mass: 31562.936 Da / Num. of mol.: 1 / Fragment: UNP residues 148-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-12, MTERFD1 / Plasmid: pNIC28-Bsa4;EF198106 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q96E29
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.2
Details: 100 mM sodium/potassium phosphate [pH 6.2], 200 mM sodium chloride, 30 % (w/v) polyethylene glycol (PEG) 300, and 1 mM dithiothreitol (DTT), VAPOR DIFFUSION, temperature 296K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9729 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 40085 / Num. obs: 39570 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.051 / Net I/σ(I): 14.85
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.92 / Num. unique all: 2867 / Rsym value: 0.642 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→41.79 Å / SU ML: 0.19 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1878 4.97 %RANDOM
Rwork0.1732 ---
obs0.1746 37761 94.27 %-
all-40056 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.954 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.822 Å20 Å2-2.883 Å2
2--7.496 Å20 Å2
3----5.673 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2222 0 0 263 2485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142266
X-RAY DIFFRACTIONf_angle_d1.4563050
X-RAY DIFFRACTIONf_dihedral_angle_d15.914865
X-RAY DIFFRACTIONf_chiral_restr0.095349
X-RAY DIFFRACTIONf_plane_restr0.008385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64320.30071280.25742373X-RAY DIFFRACTION83
1.6432-1.69160.23981300.22162483X-RAY DIFFRACTION84
1.6916-1.74620.25271390.19692563X-RAY DIFFRACTION90
1.7462-1.80860.20031310.18172624X-RAY DIFFRACTION90
1.8086-1.8810.20791620.17582690X-RAY DIFFRACTION93
1.881-1.96660.21331310.17792775X-RAY DIFFRACTION95
1.9666-2.07030.19051550.15592823X-RAY DIFFRACTION97
2.0703-2.20.1621260.15592851X-RAY DIFFRACTION97
2.2-2.36990.20871530.15422872X-RAY DIFFRACTION98
2.3699-2.60830.20231490.16022903X-RAY DIFFRACTION99
2.6083-2.98560.20711440.16892931X-RAY DIFFRACTION99
2.9856-3.76120.1941610.17152943X-RAY DIFFRACTION100
3.7612-41.80450.17921690.17253052X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8703-0.09712.08371.2947-1.4904-0.22840.2074-0.54-0.2068-0.1024-0.04980.15410.4278-0.2915-0.09390.3680.00820.15960.3672-0.02380.34032.30653.427743.6078
21.92340.7730.85510.601-0.85791.42080.049-0.0502-0.4423-0.01310.15370.38810.1518-0.1373-0.14630.1155-0.00980.03630.0937-0.00480.20597.4304-0.074131.639
30.54330.20960.0266-0.6522-1.1390.87030.0202-0.10860.1250.31550.09180.2066-0.2906-0.0146-0.22820.19930.02680.0980.083-0.01430.21413.114510.3137.8797
41.71631.22580.10180.28410.06310.68540.0216-0.06360.19530.056-0.02120.1194-0.0349-0.047-0.00570.13490.00910.03450.055-0.0070.209918.597111.388528.6377
53.49221.5753-0.48620.28530.64631.2336-0.19250.35090.2271-0.37530.13690.0415-0.2207-0.10530.02740.2022-0.00160.04470.12730.02950.177319.908915.884919.4493
61.48220.27571.02280.45650.31451.1506-0.01810.335-0.2382-0.04910.0774-0.1363-0.04730.2356-0.03790.1593-0.00530.0640.1638-0.04230.229530.20197.646117.0201
70.9291-0.65210.5761.73681.7122.08950.06780.2588-0.01450.01860.0575-0.23330.12630.3674-0.12880.15460.00630.05710.216-0.02780.208425.62536.18866.2982
81.66420.18341.26061.1474-0.10662.41210.01730.1656-0.03850.05190.0034-0.0256-0.09140.415-0.03040.1681-0.00930.06690.2673-0.0270.202919.11853.9521-5.5315
91.5574-0.10721.20651.21520.42910.79470.01650.08690.4306-0.17260.06150.3157-0.05310.0211-0.05620.1827-0.01620.05870.24030.00970.3296.08994.7602-13.4576
104.24032.35971.85181.916-0.11421.29750.0662-0.76460.7213-0.1342-0.06150.2753-0.0027-0.53920.00220.25940.01260.10290.3118-0.01020.4544-4.62174.1927-11.5577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 148:158)A148 - 158
2X-RAY DIFFRACTION2(chain A and resid 159:176)A159 - 176
3X-RAY DIFFRACTION3(chain A and resid 177:199)A177 - 199
4X-RAY DIFFRACTION4(chain A and resid 200:232)A200 - 232
5X-RAY DIFFRACTION5(chain A and resid 233:249)A233 - 249
6X-RAY DIFFRACTION6(chain A and resid 250:269)A250 - 269
7X-RAY DIFFRACTION7(chain A and resid 270:306)A270 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:353)A307 - 353
9X-RAY DIFFRACTION9(chain A and resid 354:389)A354 - 389
10X-RAY DIFFRACTION10(chain A and resid 390:417)A390 - 417

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