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- PDB-3tmm: TFAM imposes a U-turn on mitochondrial DNA -

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Basic information

Entry
Database: PDB / ID: 3tmm
TitleTFAM imposes a U-turn on mitochondrial DNA
Components
  • (DNA (28-MER)) x 2
  • Transcription factor A, mitochondrial
KeywordsTRANSCRIPTION/DNA / HMG / High Mobility Group / Transcription / LSP1 / DNA / Mitochondria / TRANSCRIPTION-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 / Mitochondrial protein degradation ...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 / Mitochondrial protein degradation / 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 / 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 / MAD / Resolution: 2.5001 Å
AuthorsNgo, H.B. / Kaiser, J.T. / Chan, D.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.
Authors: Ngo, H.B. / Kaiser, J.T. / Chan, D.C.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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: DNA (28-MER)
C: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)45,6343
Polymers45,6343
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-44 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.438, 81.911, 161.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Details20_bss: 99

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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: 28425.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mitochondrial / 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 DNA (28-MER)


Mass: 8786.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Oligonucleotide
#3: DNA chain DNA (28-MER)


Mass: 8422.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Oligonucleotide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 29% PEG 400, 0.15 M calcium acetate, 0.1 M sodium acetate,pH 4.2, 400 mM NDSB211, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.97864, 0.91837, 0.97898
SYNCHROTRONSSRL BL12-220.97864, 0.91837, 0.97898
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDDec 18, 2009
MARMOSAIC 325 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978641
20.918371
30.978981
ReflectionResolution: 2.5→24.192 Å / Num. obs: 15812 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.641,299.5
2.64-2.81,299.1
2.8-2.991,299.2
2.99-3.231,298.8
3.23-3.541,299.1
3.54-3.951,298.9
3.95-4.561,298.6
4.56-5.591,295.1
5.59-7.911,297.2
7.91-251,287.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5001→24.192 Å / SU ML: 0.78 / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 756 4.78 %
Rwork0.1948 --
obs0.1973 15812 98.49 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.55 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.2956 Å2-0 Å20 Å2
2---0.3081 Å20 Å2
3----5.9875 Å2
Refinement stepCycle: LAST / Resolution: 2.5001→24.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 1148 0 80 2869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072958
X-RAY DIFFRACTIONf_angle_d1.2254215
X-RAY DIFFRACTIONf_dihedral_angle_d23.2721239
X-RAY DIFFRACTIONf_chiral_restr0.064457
X-RAY DIFFRACTIONf_plane_restr0.004339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.69290.37031500.32333003X-RAY DIFFRACTION100
2.6929-2.96350.36791520.28253016X-RAY DIFFRACTION100
2.9635-3.39130.25181310.21653004X-RAY DIFFRACTION99
3.3913-4.26890.24261580.17843017X-RAY DIFFRACTION99
4.2689-24.19260.19661650.15013016X-RAY DIFFRACTION95
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)
19.53082.4716-4.54755.3277-7.13039.7530.3833-0.79751.26870.77990.31170.2801-1.5812-0.410.19530.4653-0.0008-0.24310.37710.15720.436125.27642.64926.2307
20.56-0.08150.42870.0389-0.22680.6369-0.0652-0.0979-0.2314-0.35120.1176-0.0445-0.51480.0007-0.14210.55740.021-0.1910.3976-0.05310.382540.6925-7.362335.4732
37.72781.6153.38094.272-0.96736.73580.4961-0.01940.55061.9397-0.2222-0.1928-0.04890.2561-0.31930.71520.0077-0.13840.3782-0.06290.351848.96050.848646.8327
41.8679-0.26120.67073.968-1.33472.31890.882-0.95610.54281.5963-0.1338-1.2521-0.65381.2067-0.38990.6605-0.1868-0.08140.7394-0.11220.471454.97864.875540.6697
50.6798-1.85291.24076.8713-4.26623.4533-0.8909-0.0349-0.0170.63120.6842-0.9347-0.4030.41510.37870.5530.1006-0.14480.44140.01810.512755.6096-7.233440.5213
66.7476-1.9547-1.04090.7150.16260.52970.34090.9939-1.00180.2284-0.11820.13510.5153-0.3074-1.42750.41820.0726-0.1773-0.11560.06260.155744.0287-17.416339.6262
73.6438-1.28521.76810.8155-0.80743.79720.13630.6432-0.5980.26460.21740.3571.00490.3676-0.27940.74110.0042-0.09530.2339-0.03840.361629.0795-13.042131.138
84.54125.67113.38768.49773.69672.9052-0.0706-1.3580.4080.033-0.85370.7237-1.06750.70330.70430.7033-0.0508-0.160.4696-0.05110.255121.2536-8.945825.8908
95.9238-1.02121.34258.36475.22713.9143-0.0238-0.09550.6786-0.9343-0.2513-0.1329-1.07460.01260.13660.3638-0.0164-0.17540.28530.04490.326818.6365-1.130918.8605
102.9881.91851.80097.0215.0766.7001-0.66690.6347-0.1510.80.3883-0.94560.8756-0.3053-0.16130.2504-0.095-0.16380.23870.04370.28327.33732.301617.8749
118.0433-1.69264.98972.0068-3.09376.22320.5094-0.0878-1.4786-0.84150.11470.87542.2919-0.0751-0.44880.6271-0.07470.00050.21530.06510.571537.22164.90517.0034
125.4194-1.4174-3.06797.96583.9363.85941.25430.5241-0.00420.7186-1.22021.0021-0.3923-0.19310.01150.4558-0.04370.04740.24270.17490.649547.581510.477217.6709
130.5957-1.0937-0.99276.50720.18412.07520.4086-0.0464-0.27720.0402-1.1388-1.2725-0.1334-0.18740.30890.206-0.0503-0.02010.4150.06240.633953.411518.49913.4128
145.31061.0582-1.50357.4864-3.96293.88330.2902-0.10110.60221.557-0.12970.1646-1.0157-0.4866-1.03410.38760.11710.05370.324-0.07690.332340.140936.616817.3224
150.27990.9069-0.09594.13380.33456.32260.31540.64740.518-0.4124-0.76431.2785-0.6707-0.58640.36080.26610.120.06490.4377-0.0620.585733.522138.253113.3336
165.3496-0.38523.82698.7474-5.98366.7222-0.30930.43060.43330.7653-0.006-0.4652-1.09210.44680.50720.3372-0.05390.02540.37740.11070.347246.155442.46115.9302
171.79890.93622.51024.86511.06759.2387-0.89-0.8992-0.1138-1.45120.4437-0.6309-0.3640.89150.55240.1959-0.0410.03040.4669-0.01090.618455.135832.64845.5613
181.37270.03762.70952.42452.83058.75940.09630.74950.1341-0.5713-0.5674-1.1058-0.46570.77970.32720.02590.08770.03710.43720.02870.765359.983620.66837.3257
197.93944.4202-2.08243.0968-0.10822.35171.187-0.5585-3.5140.246-1.4625-2.07810.68770.48070.26010.48830.2673-0.04290.51670.18161.583662.57019.02149.0249
205.3616-0.9099-0.24670.16030.19291.80991.05621.0793-1.0902-1.6856-0.6560.4112-0.46590.2348-0.51390.53590.223-0.17060.481-0.19841.062455.800510.87773.1496
213.3810.0574-5.35220.12630.14979.90820.16331.3616-0.376-0.4145-0.2148-0.4636-0.0516-1.43820.34410.4845-0.05620.04570.9694-0.46090.679537.502718.323-3.4283
222.4852-1.8959-1.36696.3149-1.04887.58270.56160.1804-0.17140.72140.4349-0.2142-0.7792-0.255-0.65230.40790.0639-0.0230.262-0.03680.29842.416725.247815.0422
238.83526.2749-6.20855.2793-2.41558.89951.173-0.9609-1.08431.8595-1.7980.3547-0.7731-0.06280.50131.13170.03030.25290.43270.08020.454337.572520.786929.0811
245.802-1.08992.29514.33731.23671.499-1.072-0.2760.54911.55430.33060.0805-0.2920.29590.85060.7099-0.0965-0.14960.31570.10110.480649.46225.022229.0288
250.7978-0.21750.59632.83870.12670.4275-0.43120.48980.0462-2.26660.0881-0.0449-0.81220.03830.2880.96560.076-0.12850.4278-0.08250.27145.7395-11.441728.6214
262.43541.9755-2.40775.6764-3.72893.1791-0.46311.19640.2241-1.5321.1554-0.26241.4694-1.0611-0.49331.32580.2419-0.06460.82-0.09250.217141.5962-10.473614.0264
273.8076-0.3254-3.51214.1713-3.09536.72691.73460.9771-0.87960.1017-1.0270.52270.44511.6836-0.66170.79040.117-0.30780.9983-0.49380.555247.6776-17.167214.2534
286.42724.23137.02418.10215.90818.0387-2.36590.06510.0745-1.77621.1433-0.5324-6.0934-0.42771.39831.90930.28-0.15710.3544-0.10490.16143.4863-4.50823.2347
297.86353.20430.22983.65443.82469.47710.8017-0.29591.017-1.6882-1.27740.2543-3.04890.11010.36490.96420.0076-0.02510.2393-0.02920.310644.81014.875436.9223
305.74760.02424.84660.80710.28947.46480.46230.0393-0.93680.75060.16871.65860.27-0.0934-0.97770.5877-0.1337-0.13860.07660.03750.527748.869616.567628.3413
314.6983-6.0862-0.89118.68853.21566.75250.96650.6509-0.7245-0.498-0.36110.6245-1.1097-1.2872-0.59480.37560.1527-0.03690.46210.15040.495635.193121.35118.9332
325.5625-3.8148-1.00935.4852-2.30764.9593-0.13310.8831-0.1369-0.85810.0210.44351.05450.36710.00560.30770.0865-0.04590.3363-0.04170.307337.418529.15397.1115
334.27781.31760.96065.01445.80036.99181.1110.7331-0.6812-0.8576-1.28010.12810.4135-0.90810.38690.52020.0331-0.05350.7346-0.37020.595646.013817.6129-0.3169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:7)
2X-RAY DIFFRACTION2(chain A and resid 8:19)
3X-RAY DIFFRACTION3(chain A and resid 20:31)
4X-RAY DIFFRACTION4(chain A and resid 32:39)
5X-RAY DIFFRACTION5(chain A and resid 40:48)
6X-RAY DIFFRACTION6(chain A and resid 49:63)
7X-RAY DIFFRACTION7(chain A and resid 64:72)
8X-RAY DIFFRACTION8(chain A and resid 73:77)
9X-RAY DIFFRACTION9(chain A and resid 78:85)
10X-RAY DIFFRACTION10(chain A and resid 86:91)
11X-RAY DIFFRACTION11(chain A and resid 92:99)
12X-RAY DIFFRACTION12(chain A and resid 100:106)
13X-RAY DIFFRACTION13(chain A and resid 107:116)
14X-RAY DIFFRACTION14(chain A and resid 117:137)
15X-RAY DIFFRACTION15(chain A and resid 138:149)
16X-RAY DIFFRACTION16(chain A and resid 150:162)
17X-RAY DIFFRACTION17(chain A and resid 163:167)
18X-RAY DIFFRACTION18(chain A and resid 168:179)
19X-RAY DIFFRACTION19(chain A and resid 180:185)
20X-RAY DIFFRACTION20(chain A and resid 186:191)
21X-RAY DIFFRACTION21(chain B and resid 1:4)
22X-RAY DIFFRACTION22(chain B and resid 5:10)
23X-RAY DIFFRACTION23(chain B and resid 11:14)
24X-RAY DIFFRACTION24(chain B and resid 15:20)
25X-RAY DIFFRACTION25(chain B and resid 21:24)
26X-RAY DIFFRACTION26(chain B and resid 25:28)
27X-RAY DIFFRACTION27(chain C and resid 1:4)
28X-RAY DIFFRACTION28(chain C and resid 5:8)
29X-RAY DIFFRACTION29(chain C and resid 9:12)
30X-RAY DIFFRACTION30(chain C and resid 13:16)
31X-RAY DIFFRACTION31(chain C and resid 17:20)
32X-RAY DIFFRACTION32(chain C and resid 21:24)
33X-RAY DIFFRACTION33(chain C and resid 25:28)

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