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- PDB-4nnu: Distinct structural features of TFAM drive mitochondrial DNA pack... -

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Basic information

Entry
Database: PDB / ID: 4nnu
TitleDistinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation
Components
  • DNA1
  • DNA2
  • Transcription factor A, mitochondrial
KeywordsTRANSCRIPTION/DNA / HMG / DNA bending / TFB2M / mtRNAP / mitochondrial / TRANSCRIPTION-DNA complex
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: 2.81 Å
AuthorsNgo, H.B. / Lovely, G.A. / Phillips, R. / Chan, D.C.
CitationJournal: Nat Commun / Year: 2014
Title: Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation.
Authors: Ngo, H.B. / Lovely, G.A. / Phillips, R. / Chan, D.C.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: DNA1
E: DNA1
D: DNA2
F: DNA2


Theoretical massNumber of molelcules
Total (without water)81,1446
Polymers81,1446
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17200 Å2
ΔGint-98 kcal/mol
Surface area33890 Å2
MethodPISA
2
A: Transcription factor A, mitochondrial
C: DNA1
D: DNA2


Theoretical massNumber of molelcules
Total (without water)40,5723
Polymers40,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-42 kcal/mol
Surface area18550 Å2
MethodPISA
3
B: Transcription factor A, mitochondrial
E: DNA1
F: DNA2


Theoretical massNumber of molelcules
Total (without water)40,5723
Polymers40,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-46 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.800, 114.380, 144.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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: 27067.166 Da / Num. of mol.: 2 / Fragment: UNP residues 43-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF6, TCF6L2, TFAM / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q00059
#2: DNA chain DNA1


Mass: 6823.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFAM / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: DNA chain DNA2


Mass: 6681.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNA / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 9% PEG1500 and 18% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2012
RadiationMonochromator: Rh coated / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.81→36.87 Å / Num. obs: 22010 / % possible obs: 30 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TQ6

3tq6


Resolution: 2.81→36.017 Å / SU ML: 0.54 / σ(F): 1.36 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 1988 9.04 %Random
Rwork0.2137 ---
all0.219 22010 --
obs0.2181 21991 97.41 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.46 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.8471 Å20 Å20 Å2
2--5.8153 Å20 Å2
3---2.6158 Å2
Refinement stepCycle: LAST / Resolution: 2.81→36.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 1804 0 30 5077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065325
X-RAY DIFFRACTIONf_angle_d1.3637529
X-RAY DIFFRACTIONf_dihedral_angle_d23.0572219
X-RAY DIFFRACTIONf_chiral_restr0.068813
X-RAY DIFFRACTIONf_plane_restr0.004649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8088-2.8790.57071210.50241239X-RAY DIFFRACTION86
2.879-2.95690.49731450.44431434X-RAY DIFFRACTION99
2.9569-3.04380.43691520.35861418X-RAY DIFFRACTION99
3.0438-3.1420.35441400.29611435X-RAY DIFFRACTION99
3.142-3.25420.33091320.25451452X-RAY DIFFRACTION99
3.2542-3.38440.31281430.23091417X-RAY DIFFRACTION99
3.3844-3.53830.25291430.22231429X-RAY DIFFRACTION98
3.5383-3.72470.28891450.21631403X-RAY DIFFRACTION97
3.7247-3.95780.23391430.22231457X-RAY DIFFRACTION99
3.9578-4.2630.23361430.19561434X-RAY DIFFRACTION99
4.263-4.69110.25361450.17051464X-RAY DIFFRACTION99
4.6911-5.3680.2191420.17141443X-RAY DIFFRACTION97
5.368-6.75580.23981480.19461455X-RAY DIFFRACTION98
6.7558-36.020.17261460.15661523X-RAY DIFFRACTION97
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)
13.34591.6947-0.53043.0863-0.50131.31510.20280.01290.16660.2504-0.2024-0.2905-0.17170.08420.06660.29740.01470.02020.332-0.03310.4612-19.7085-3.1842-28.6811
24.97261.2316-6.70670.5203-1.83457.11730.77180.12220.28440.2568-0.3464-0.2492-0.66790.0994-0.450.39360.0070.07370.3990.0110.5567-19.2078-23.7046-40.3553
33.10830.65963.37771.07821.49425.77560.07280.30230.111-0.1753-0.03830.10540.4086-0.4545-0.11970.454-0.0078-0.02390.75580.0710.4236-7.3061-32.0958-63.7142
42.5972-0.2356-1.37032.59590.53090.53220.1907-0.2468-0.7930.3172-0.3049-0.208-0.0155-0.11230.02210.4363-0.0401-0.12590.4130.13320.6867-18.5805-58.8629-38.6787
53.4704-0.6547-0.68734.21531.63613.72250.46850.51360.0486-0.2687-0.5-0.5248-0.05780.30380.04620.2925-0.09990.05210.25330.09470.4082-20.9179-55.0935-48.0437
64.7489-0.98726.28571.7778-1.61437.15510.71590.3857-0.2107-0.125-0.5473-0.35280.39410.462-0.07370.3630.01260.01230.40790.00510.462-18.8282-35.6543-34.3626
72.5646-0.3021-2.04982.41261.20993.89260.0188-0.8772-0.27180.71190.0283-0.0716-0.1866-0.2945-0.12840.54910.0607-0.02811.12540.02250.4843-5.2087-27.1784-11.7779
84.5408-3.0993-0.06786.46341.2394.85641.05810.8717-0.9325-1.4503-0.7941-0.114-0.07450.7722-0.26070.77890.2367-0.03950.67710.01650.7253-15.0053-6.6163-41.6276
91.6488-2.00581.73384.2304-0.25183.3517-0.7972-0.91250.05120.99770.47440.5303-1.7417-0.60580.25081.03480.1751-0.03490.81520.08750.5304-16.7512-28.9003-57.6415
104.95012.4343-0.2624.66351.87781.56930.9173-1.54021.09981.7522-0.70560.15010.1780.6227-0.43691.0888-0.2254-0.08150.87480.14890.8018-14.5259-52.1508-32.5172
110.88160.7169-0.9742.13181.29862.9814-0.4069-0.5459-0.61720.99290.09370.36160.8034-0.1280.39850.89870.11890.1710.98630.12990.6543-15.4586-30.1102-17.0434
120.86690.99380.77421.7834-1.02883.3430.6232-0.15560.17450.8375-0.72390.9242-1.36230.2250.11380.74270.08590.16250.53120.22080.7286-17.2099-25.068-57.6743
134.71931.2021-0.28913.5186-3.57897.13520.10321.0623-0.6887-0.9647-0.0879-1.03751.90070.5861-0.07410.63360.09390.03830.6024-0.06470.7304-11.6133-8.4246-36.646
140.53440.20650.41470.60611.34022.68230.9296-0.9866-0.4438-0.4592-1.24550.51411.9380.38760.45181.018-0.0863-0.14990.83010.37780.9806-15.7754-34.3268-16.7796
155.8130.0482-1.21373.7532-2.872.85370.5755-0.99121.13090.7518-0.2415-0.4998-1.91731.4748-0.16530.7624-0.1030.13670.7020.06520.8645-11.7463-50.6919-37.7503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 44:122)
2X-RAY DIFFRACTION2chain 'A' and (resseq 123:151)
3X-RAY DIFFRACTION3chain 'A' and (resseq 152:236)
4X-RAY DIFFRACTION4chain 'B' and (resseq 44:76)
5X-RAY DIFFRACTION5chain 'B' and (resseq 77:122)
6X-RAY DIFFRACTION6chain 'B' and (resseq 123:151)
7X-RAY DIFFRACTION7chain 'B' and (resseq 152:234)
8X-RAY DIFFRACTION8chain 'C' and (resseq 1:9)
9X-RAY DIFFRACTION9chain 'C' and (resseq 10:22)
10X-RAY DIFFRACTION10chain 'E' and (resseq 1:9)
11X-RAY DIFFRACTION11chain 'E' and (resseq 10:22)
12X-RAY DIFFRACTION12chain 'D' and (resseq 1:13)
13X-RAY DIFFRACTION13chain 'D' and (resseq 14:22)
14X-RAY DIFFRACTION14chain 'F' and (resseq 1:13)
15X-RAY DIFFRACTION15chain 'F' and (resseq 14:22)

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