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- PDB-6hb4: TFAM in Complex with Site-Y -

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Basic information

Entry
Database: PDB / ID: 6hb4
TitleTFAM in Complex with Site-Y
Components
  • DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
  • DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
  • Transcription factor A, mitochondrial
KeywordsDNA BINDING PROTEIN / HMG-box / Transcription activator / Mitochondrial DNA / mtDNA Control region / DNA Compaction
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
DNA / DNA (> 10) / Transcription factor A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsCuppari, A. / Fernandez-Millan, P. / Rubio-Cosials, A. / Tarres-Sole, A. / Lyonnais, S. / Sola, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2015-70645-R Spain
Citation
Journal: 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.
#1: Journal: 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
DepositionAug 9, 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 1.2Jan 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_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: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
C: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
D: Transcription factor A, mitochondrial
E: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
F: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
G: Transcription factor A, mitochondrial
H: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
I: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
J: Transcription factor A, mitochondrial
K: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
L: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,74718
Polymers156,60912
Non-polymers1,1376
Water00
1
A: Transcription factor A, mitochondrial
B: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
C: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8137
Polymers39,1523
Non-polymers6614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-46 kcal/mol
Surface area18650 Å2
MethodPISA
2
D: Transcription factor A, mitochondrial
E: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
F: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3914
Polymers39,1523
Non-polymers2381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-44 kcal/mol
Surface area18590 Å2
MethodPISA
3
G: Transcription factor A, mitochondrial
H: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
I: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3914
Polymers39,1523
Non-polymers2381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-32 kcal/mol
Surface area18560 Å2
MethodPISA
4
J: Transcription factor A, mitochondrial
K: DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')
L: DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)39,1523
Polymers39,1523
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-32 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.669, 140.622, 108.919
Angle α, β, γ (deg.)90.00, 130.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: 25651.559 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
#2: DNA chain
DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A)-3')


Mass: 6741.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: mitochondrial DNA / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)-3')


Mass: 6759.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: mitochondrial DNA / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 23-28% PEG 3350, 0.08-0.2M ammonium acetate, and 0.1 M bis-Tris pH 6.5 or Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.93928 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: 0.93928 Å / Relative weight: 1
ReflectionResolution: 3.05→43.7 Å / Num. obs: 34352 / % possible obs: 99.96 % / Redundancy: 13.6 % / Biso Wilson estimate: 81.52 Å2 / Rsym value: 0.103 / Net I/σ(I): 19.4
Reflection shellResolution: 3.05→3.14 Å / Num. unique obs: 2796

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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: 3.05→43.05 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9037 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.384
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1733 5.05 %RANDOM
Rwork0.19 ---
obs0.1924 34312 99.96 %-
Displacement parametersBiso mean: 88.24 Å2
Baniso -1Baniso -2Baniso -3
1--6.1226 Å20 Å2-3.9888 Å2
2---7.8712 Å20 Å2
3---13.9938 Å2
Refine analyzeLuzzati coordinate error obs: 0.57 Å
Refinement stepCycle: LAST / Resolution: 3.05→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6551 3793 76 0 10420
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01211001HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.5215561HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4824SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes185HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1127HARMONIC5
X-RAY DIFFRACTIONt_it11001HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion22.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1392SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11979SEMIHARMONIC4
LS refinement shellResolution: 3.05→3.14 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2847 148 5.03 %
Rwork0.2455 2796 -
all0.2475 2944 -
obs--99.96 %
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)
10.53340.73140.29651.1420.99880.6315-0.00170.0460.04830.0464-0.00490.0321-0.0802-0.06140.0066-0.0362-0.04660.0225-0.0395-0.0170.0661-16.12331.9241-40.4039
20.19390.04080.42811.6693-0.14040.5935-0.00630.0033-0.016-0.0077-0.0005-0.00150.0143-0.00040.00680.0129-0.0174-0.0245-0.00830.00990.0143-12.634735.9579-40.8935
30.05481.16720.01021.33640.54271.1727-0.034-0.0056-0.00240.02170.00050.00180.00810.01770.03350.0121-0.0185-0.0304-0.00190.0071-0.0077-14.027535.2511-40.8461
41.94641.01230.35120.4850.36690.3569-0.0303-0.0363-0.01060.09530.11120.00590.12750.0248-0.0809-0.0275-0.07010.03430.0108-0.055-0.0181-5.225716.213-20.0356
50.11760.110.23320.8698-1.04391.11260.0051-0.01120.0182-0.00280.0216-0.01230.00080.0151-0.02670.0448-0.0118-0.0205-0.00610.0088-0.0144-9.08512.1001-22.1108
61.01950.50040.11981.26860.0072-0.39630.00630.00270.005-0.01450.0114-0.00190.0117-0.0126-0.01770.04160.0023-0.0247-0.0030.0232-0.0293-7.405212.6599-20.1678
70.71850.74060.2590.80570.47190.2742-0.00620.0322-0.05350.0095-0.0110.02030.0413-0.0150.01720.04150.01540.00040.012-0.0792-0.0734-40.17715.270312.7854
81.43090.9107-0.63590.590.2644-0.4529-0.01020.02270.00920.00170.0235-0.00840.0167-0.0238-0.01330.0149-0.0494-0.0091-0.0085-0.0781-0.0107-38.87852.53479.9778
91.82111.3744-0.13180.69940.911-0.53330.01480.01390.0051-0.00390.0210.02010.0131-0.0181-0.03580.0289-0.0379-0.0233-0.0074-0.0863-0.014-39.77731.243910.1123
100.17790.13790.14960.06351.07382.4294-0.0324-0.01560.0643-0.00880.04870.0801-0.0145-0.0504-0.0162-0.0872-0.02920.05130.0427-0.08280.008-60.548320.71221.8498
111.0146-1.0939-0.365600.70290.3463-0.01160.0107-0.0012-0.01630.00540.00750.0098-0.01340.00620.0010.00790.0050.008-0.02460.0014-57.489225.16796.1865
12-0.80630.6042-0.72530.00180.66482.7723-0.0188-0.01560.0214-0.01380.0204-0.01120.01090.0007-0.0016-0.02350.00350.00270.0284-0.02020.0073-60.183123.7633.459
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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