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

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Basic information

Entry
Database: PDB / ID: 4nod
TitleDistinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation
Components
  • 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
  • Transcription factor A, mitochondrial
KeywordsTRANSCRIPTION REGULATOR/DNA / HMG / DNA bending / TFB2M / mtRNAP / BrU substitution to HSP1 / T19 / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription factor activity / 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 promoter sequence-specific DNA binding / mitochondrial transcription factor activity / 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: 2.897 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
E: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'
F: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'
G: Transcription factor A, mitochondrial
H: Transcription factor A, mitochondrial
I: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
K: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
J: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'
L: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)162,55112
Polymers162,55112
Non-polymers00
Water00
1
A: Transcription factor A, mitochondrial
C: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)40,6383
Polymers40,6383
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-27 kcal/mol
Surface area18830 Å2
MethodPISA
2
B: Transcription factor A, mitochondrial
E: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
F: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)40,6383
Polymers40,6383
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-27 kcal/mol
Surface area18740 Å2
MethodPISA
3
G: Transcription factor A, mitochondrial
I: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
J: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)40,6383
Polymers40,6383
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-28 kcal/mol
Surface area18680 Å2
MethodPISA
4
H: Transcription factor A, mitochondrial
K: 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'
L: 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)40,6383
Polymers40,6383
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-28 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.372, 82.490, 104.222
Angle α, β, γ (deg.)79.86, 85.48, 84.53
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31G
41H
12C
22E
32I
42K
13D
23F
33J
43L

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARGAA44 - 23337 - 226
21SERSERARGARGBB44 - 23337 - 226
31SERSERARGARGGG44 - 23337 - 226
41SERSERARGARGHH44 - 23337 - 226
12DTDTDGDGCC1 - 221 - 22
22DTDTDGDGED1 - 221 - 22
32DTDTDGDGII1 - 221 - 22
42DTDTDGDGKJ1 - 221 - 22
13DCDCDADADE1 - 221 - 22
23DCDCDADAFF1 - 221 - 22
33DCDCDADAJK1 - 221 - 22
43DCDCDADALL1 - 221 - 22

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.970039, -0.19578, -0.143856), (-0.195589, -0.980562, 0.015606), (-0.144115, 0.012998, -0.989476)7.32416, 76.74743, -4.31803
3given(-0.968563, 0.21758, 0.120603), (0.201373, 0.401085, 0.893633), (0.146064, 0.889826, -0.432291)9.28099, -9.99275, 11.92094
4given(-0.999794, -0.01821, -0.008953), (0.015892, -0.428291, -0.903501), (0.012618, -0.903457, 0.428492)17.22186, 84.29516, -18.33994

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Components

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


Mass: 27067.166 Da / Num. of mol.: 4 / 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
5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP*(BRU)P*TP*GP*G)-3'


Mass: 7006.313 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Heavy Strand Promoter 1 (HSP1) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: DNA chain
5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP*CP*CP*AP*A)-3'


Mass: 6564.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Heavy Strand Promoter 1 (HSP1) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG8000, 22% glycerol, 0.04 M potassium phosphate monobasic, pH 6, 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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2012 / Details: Rh coated mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.897→39 Å / Num. all: 40810 / Num. obs: 35526 / % possible obs: 50 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 13.5
Reflection shellHighest resolution: 2.897 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TQ6

3tq6


Resolution: 2.897→35.64 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 39.673 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26744 1783 5 %RANDOM
Rwork0.22108 ---
all0.267 ---
obs0.22345 33743 87.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.732 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å2-0.23 Å2-0.16 Å2
2--2.59 Å25 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.897→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 3577 0 0 9985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01610539
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.65714907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9565756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15623.875320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.385151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8221560
X-RAY DIFFRACTIONr_chiral_restr0.0940.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216651
X-RAY DIFFRACTIONr_mcbond_it5.717.5973036
X-RAY DIFFRACTIONr_mcangle_it8.90611.383788
X-RAY DIFFRACTIONr_scbond_it6.9918.9897503
X-RAY DIFFRACTIONr_long_range_B_refined15.69177.20917072
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A160218.17
12B160212.44
13G160216.1
14H160213.22
21C45912.14
22E45917.58
23I45913.72
24K45912.43
31D43413.8
32F43412.17
33J43412.11
34L43411.86
LS refinement shellResolution: 2.897→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 131 -
Rwork0.418 2505 -
obs--86.4 %
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)
10.130.1803-0.4380.2583-0.61861.50570.0680.03470.01670.10350.0080.0336-0.2891-0.0701-0.0760.12220.03060.00380.14590.00430.0847-4.082553.1991-6.6398
20.2259-0.18750.42370.1592-0.35950.84380.0425-0.0148-0.0617-0.03150.03740.04450.1168-0.0988-0.07990.0722-0.03770.01520.1677-0.00830.0957-6.126125.29333.573
30.02580.0008-0.15230.1188-0.10581.03020.02650.005-0.02280.1061-0.1285-0.0243-0.29020.01620.1020.1618-0.04770.00570.2310.09620.0867-3.049655.4587-5.3409
40.29650.25150.09830.2460.17281.5517-0.05330.0166-0.0082-0.0414-0.0417-0.04720.1830.12040.0950.07580.08030.01310.17070.07490.1022-5.856522.89661.9589
50.32360.5129-0.90420.8259-1.44912.55060.1925-0.01180.03490.3638-0.01470.0946-0.62880.0127-0.17780.17930.06260.04640.2540.12040.1243-4.032354.5466-8.4342
60.2992-0.32580.60910.4177-0.73421.32530.07780.01730.0058-0.21530.01880.06190.3422-0.0237-0.09660.2741-0.0401-0.0270.21540.12570.1206-6.207623.87335.0634
70.14060.2331-0.28480.3951-0.47330.60060.0457-0.0357-0.00490.0782-0.0398-0.0354-0.07530.0477-0.00590.0922-0.0119-0.01130.0836-0.04490.102122.95935.919662.8852
80.0687-0.20390.23790.65-0.68850.83710.049-0.0049-0.014-0.19740.0369-0.01710.1763-0.0179-0.0860.1145-0.00570.00240.0622-0.04390.118920.94663.137233.2967
90.11350.3942-0.21691.7941-0.43710.8290.07150.07740.0490.20650.17230.1203-0.1703-0.1548-0.24380.11750.02240.04780.1126-0.00060.101622.7198.401464.4733
100.12450.14260.15861.1133-0.58310.83460.0309-0.0531-0.0268-0.1770.09060.03130.2316-0.1686-0.12160.182-0.0104-0.03790.1037-0.01760.082120.04860.811731.7523
110.28440.4547-0.48850.735-0.78410.84740.0809-0.01120.02430.1458-0.01970.0573-0.17030.0431-0.06120.1888-0.0146-0.04290.13540.01550.056923.03265.127664.869
120.308-0.45590.42890.6771-0.63710.61540.0619-0.044-0.0146-0.1240.01980.02780.1581-0.0396-0.08170.2466-0.035-0.0060.1368-0.01680.074320.9774.09831.2636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 233
2X-RAY DIFFRACTION2B44 - 233
3X-RAY DIFFRACTION3C1 - 22
4X-RAY DIFFRACTION4E1 - 22
5X-RAY DIFFRACTION5D1 - 22
6X-RAY DIFFRACTION6F1 - 22
7X-RAY DIFFRACTION7G44 - 233
8X-RAY DIFFRACTION8H44 - 233
9X-RAY DIFFRACTION9I1 - 22
10X-RAY DIFFRACTION10K1 - 22
11X-RAY DIFFRACTION11J1 - 22
12X-RAY DIFFRACTION12L1 - 22

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