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- PDB-3tq6: Crystal structure of human mitochondrial transcription factor A, ... -

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Basic information

Entry
Database: PDB / ID: 3tq6
TitleCrystal structure of human mitochondrial transcription factor A, TFAM or mtTFA, bound to the light strand promoter LSP
Components
  • DNA (5'-D(*GP*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*(BRU)P*AP*AP*C)-3')
  • Transcription factor A, mitochondrial
KeywordsTRANSCRIPTION/DNA / Transcription / Transcription regulation / Mitochondrion / DNA-binding / HMGB-UBF_HMG-box / minor groove / tandem HMG boxes / TRANSCRIPTION-DNA complex / mitochondrial nucleoid / light-strand mitochondrial promoter / LSP
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / mitochondrial transcription / DNA binding, bending / mitochondrial nucleoid / heat shock protein binding / response to nutrient ...Mitochondrial transcription initiation / mitochondrial transcription factor activity / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / mitochondrial transcription / DNA binding, bending / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Mitochondrial protein degradation / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / mitochondrion / RNA binding / nucleus / cytosol
Similarity search - Function
: / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DNA / DNA (> 10) / Transcription factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRubio-Cosials, A. / Sydow, J.F. / Jimenez-Menendez, N. / Fernandez-Millan, P. / Montoya, J. / Jacobs, H.T. / Coll, M. / Bernado, P. / Sola, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter.
Authors: Rubio-Cosials, A. / Sidow, J.F. / Jimenez-Menendez, N. / Fernandez-Millan, P. / Montoya, J. / Jacobs, H.T. / Coll, M. / Bernado, P. / Sola, M.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Jan 11, 2017Group: Other
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,9949
Polymers78,5546
Non-polymers4393
Water3,351186
1
A: Transcription factor A, mitochondrial
C: DNA (5'-D(*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*(BRU)P*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3724
Polymers39,2773
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-41 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: Transcription factor A, mitochondrial
E: DNA (5'-D(*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*(BRU)P*AP*AP*C)-3')
F: DNA (5'-D(*GP*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6225
Polymers39,2773
Non-polymers3442
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-34 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.900, 117.200, 56.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcription factor A, mitochondrial / mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / ...mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / Transcription factor 6-like 2


Mass: 25708.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR407653.1, TCF6, TCF6L2, TFAM / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q00059

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*(BRU)P*AP*AP*C)-3')


Mass: 6659.169 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. DNA nt 424-445 LSP
Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*A)-3')


Mass: 6909.445 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans. Complementary DNA nt 424-445 LSP
Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 189 molecules

#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 37.5% (v/v) PEG1000, 300 mM sodium chloride, 0.1 M Na,K-phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2010
Details: Focusing mirrors: one pair of (300x40x15) mm3 long Pt coated Si mirror, 260mm usable, in a Kirkpatrick-Baez geometry;
RadiationMonochromator: monochromator (horizontally side diffracting Silicon 111 crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.45→40.84 Å / Num. obs: 28529 / % possible obs: 99.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.6 / Redundancy: 7 % / Biso Wilson estimate: 59.217 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.049 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.45-2.577.40.4674.2303500.467100
2.58-2.737.30.3345.9282680.33499.9
2.74-2.927.30.2268.3267530.226100
2.93-3.157.10.1412.6243770.1499.9
3.16-3.456.90.08119.8216130.08199.7
3.46-3.866.70.06224.8192580.06299.9
3.87-4.466.60.04830.7168500.04899.7
4.47-5.476.60.04233.6144760.04299.8
5.48-7.746.50.03835.1113110.038100
7.75-406.10.03140.761620.03198.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→40.84 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9137 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 992 3.48 %RANDOM
Rwork0.1816 ---
obs0.1832 28483 --
all-2954 --
Displacement parametersBiso mean: 41.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.9362 Å20 Å20 Å2
2---8.0574 Å20 Å2
3---4.1212 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: LAST / Resolution: 2.45→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 1792 28 186 5243
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125380HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.47593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d22293SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes2108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5588HARMONIC5
X-RAY DIFFRACTIONt_it205380HARMONIC20
X-RAY DIFFRACTIONt_nbd50SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.65
X-RAY DIFFRACTIONt_chiral_improper_torsion5686SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance194HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact45465SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2836 103 3.49 %
Rwork0.2084 2851 -
all0.2111 2954 -
obs-28483 3.48 %
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)
10.8527-0.56120.39340.7703-0.27890.38160.0796-0.03130.0827-0.1221-0.0259-0.0886-0.0674-0.0425-0.0537-0.0330.01020.0543-0.0101-0.0191-0.1198-22.215133.8141-15.0633
20.4205-0.6371-0.23991.23880.1050.60450.03620.0111-0.0172-0.093-0.00430.1290.0077-0.0886-0.0319-0.11130.0174-0.03190.0013-0.0028-0.0847-47.590519.7731-10.5944
32.3396-1.04070.80842.8134-1.338900.02050.0122-0.09670.0312-0.1207-0.25110.0262-0.13270.1003-0.06080.00790.0558-0.0478-0.0011-0.0023-24.013638.4397-14.8951
41.6322-2.76070.87473.3082-0.3390-0.0367-0.0502-0.12930.0442-0.0705-0.06090.1292-0.09870.1072-0.0216-0.00390.056-0.02110.0186-0.0262-22.395736.1384-15.0827
51.6481-2.09840.32042.9159-0.8070-0.00070.0531-0.0409-0.01320.04730.1758-0.07070.0739-0.0467-0.07010.0047-0.0217-0.00840.03740.0073-45.512315.3216-9.2941
63.6447-4.64031.16585.125-1.66260.4432-0.0069-0.0456-0.0108-0.0040.030.2291-0.252-0.0649-0.0231-0.10010.0301-0.0140.04710.0178-0.0992-47.029217.3789-10.2617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A44 - 237
2X-RAY DIFFRACTION2{ B|* }B44 - 233
3X-RAY DIFFRACTION3{ C|* }C1 - 22
4X-RAY DIFFRACTION4{ D|* }D1 - 22
5X-RAY DIFFRACTION5{ E|* }E1 - 22
6X-RAY DIFFRACTION6{ F|* }F1 - 22

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