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- PDB-6hc3: TFAM bound to Site-X -

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Basic information

Entry
Database: PDB / ID: 6hc3
TitleTFAM bound to Site-X
Components
  • DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
  • DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
  • Transcription factor A, mitochondrial
KeywordsDNA BINDING PROTEIN / Transcription factor / DNA compaction / mitochondria / mitochondrial DNA
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial transcription / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Transcriptional activation of mitochondrial biogenesis ...Mitochondrial transcription initiation / mitochondrial promoter sequence-specific DNA binding / mitochondrial respiratory chain complex assembly / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial transcription / mitochondrial nucleoid / heat shock protein binding / response to nutrient / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / 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
L(+)-TARTARIC ACID / DNA / DNA (> 10) / Transcription factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFernandez-Millan, P. / Cuppari, A. / Tarres-Sole, A. / Rubio-Cosials, A. / Lyonnais, S. / Sola, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2015-70645-R Spain
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region.
Authors: Cuppari, A. / Fernandez-Millan, P. / Battistini, F. / Tarres-Sole, A. / Lyonnais, S. / Iruela, G. / Ruiz-Lopez, E. / Enciso, Y. / Rubio-Cosials, A. / Prohens, R. / Pons, M. / Alfonso, C. / ...Authors: Cuppari, A. / Fernandez-Millan, P. / Battistini, F. / Tarres-Sole, A. / Lyonnais, S. / Iruela, G. / Ruiz-Lopez, E. / Enciso, Y. / Rubio-Cosials, A. / Prohens, R. / Pons, M. / Alfonso, C. / Toth, K. / Rivas, G. / Orozco, M. / Sola, M.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2019Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.3Jan 17, 2024Group: 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
A: Transcription factor A, mitochondrial
B: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
C: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
D: Transcription factor A, mitochondrial
E: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
F: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
G: Transcription factor A, mitochondrial
H: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
I: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
J: Transcription factor A, mitochondrial
K: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
L: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,67121
Polymers161,96812
Non-polymers1,7049
Water21612
1
A: Transcription factor A, mitochondrial
B: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
C: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1807
Polymers40,4923
Non-polymers6894
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-34 kcal/mol
Surface area18620 Å2
MethodPISA
2
D: Transcription factor A, mitochondrial
E: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
F: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8805
Polymers40,4923
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-33 kcal/mol
Surface area18490 Å2
MethodPISA
3
G: Transcription factor A, mitochondrial
H: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
I: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8805
Polymers40,4923
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-40 kcal/mol
Surface area18550 Å2
MethodPISA
4
J: Transcription factor A, mitochondrial
K: DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')
L: DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7304
Polymers40,4923
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-37 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.790, 145.136, 108.119
Angle α, β, γ (deg.)90.00, 130.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ADGJ

#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: 26993.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFAM, TCF6, TCF6L2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00059

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DNA chain , 2 types, 8 molecules BEHKCFIL

#2: DNA chain
DNA/RNA (5'-D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)-3')


Mass: 6665.385 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)-3')


Mass: 6833.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 21 molecules

#4: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C4H6O6
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 18-24% PEG 3350, sodium potassium tartrate 0.1-0.25M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→42.21 Å / Num. obs: 34552 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 58.53 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.9
Reflection shellResolution: 3.1→42.21 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tq6

3tq6


Resolution: 3.1→42.21 Å / Cor.coef. Fo:Fc: 0.9208 / Cor.coef. Fo:Fc free: 0.8781 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.382
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1732 5.01 %RANDOM
Rwork0.1878 ---
obs0.1899 34547 98.9 %-
Refine analyzeLuzzati coordinate error obs: 0.505 Å
Refinement stepCycle: 1 / Resolution: 3.1→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 3743 107 12 10560
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01211123HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3815713HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5623SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes195HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1167HARMONIC5
X-RAY DIFFRACTIONt_it11123HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion4.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance182HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11895SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.19 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.311 145 4.85 %
Rwork0.2337 2845 -
all0.2373 2990 -
obs--98.9 %
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)
10.97460.69410.81951.42170.76240.68850.0360.0168-0.09510.0585-0.05650.06090.00330.07960.02050.062-0.03090.0084-0.0381-0.0927-0.0964-41.75734.323311.7687
20.4127-0.16490.06111.5138-0.03330.41870.04270.02260.01340.0107-0.0110.013-0.04230.0034-0.03180.0289-0.0314-0.0257-0.0295-0.0927-0.0304-40.69940.38328.3705
30.49330.63170.44781.46120.26270.40550.0699-0.0020.0010.0191-0.00860.0409-0.03190.0249-0.06130.0371-0.0317-0.0379-0.0179-0.079-0.0336-39.97182.35111.6875
4-0.0437-0.01590.38020.52420.42610.8361-0.0120.00280.06220.03340.04590.0986-0.0473-0.029-0.034-0.1037-0.05030.05050.0464-0.0130.114-62.628222.85153.9679
50.0868-0.0332-0.01430.1139-0.13930.47790.0154-0.0020.0120.0253-0.0110.0038-0.030.0093-0.0045-0.0016-0.0180.00320.0156-0.00390.0239-62.458924.89283.4884
6-0.2584-0.3447-0.15160.00010.62711.24320.0093-0.02810.00860.0060.00180.014-0.01050.0019-0.0111-0.01780.00070.00120.01160.0190.0442-64.345321.67631.8757
70.9998-0.35490.18990.50890.0216-0.0411-0.03210.0259-0.0572-0.10870.0362-0.01670.0746-0.0083-0.00410.12680.02740.01880.03970.0483-0.11526.625613.585119.0096
80.0732-0.27230.10560.05680.12340.1779-0.00440.0012-0.016-0.0093-0.0056-0.01350.00930.00060.010.0309-0.00460.00170.01820.012-0.00178.81498.493321.2325
91.2232-0.4401-0.3300.6135-0.1927-0.00740.0025-0.005-0.01250.002-0.00360.00620.0290.00540.0386-0.0148-0.00760.007-0.0046-0.01194.42314.504917.6834
100.8693-0.90070.79321.4876-0.55880.75030.0101-0.08290.0148-0.0642-0.0576-0.0551-0.0993-0.00870.0475-0.10550.08980.0335-0.02630.02430.062917.439531.897738.6315
110.40080.0405-0.01961.5364-0.06320.515-0.0315-0.0059-0.0357-0.0071-0.0137-0.0120.0264-0.02330.0452-0.03430.0901-0.0162-0.02880.02750.031814.143435.766740.1965
120.5787-0.28260.44381.3728-0.65490.335-0.0601-0.0237-0.0091-0.0416-0.0049-0.01390.01870.00290.065-0.03970.0751-0.0238-0.01870.01960.045417.528233.788840.4502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|' }
2X-RAY DIFFRACTION2{ B|' }
3X-RAY DIFFRACTION3{ C|' }
4X-RAY DIFFRACTION4{ D|' }
5X-RAY DIFFRACTION5{ E|' }
6X-RAY DIFFRACTION6{ F|' }
7X-RAY DIFFRACTION7{ G|' }
8X-RAY DIFFRACTION8{ H|' }
9X-RAY DIFFRACTION9{ I|' }
10X-RAY DIFFRACTION10{ J|' }
11X-RAY DIFFRACTION11{ K|' }
12X-RAY DIFFRACTION12{ L|' }

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