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- PDB-5ol9: Structure of human mitochondrial transcription elongation factor ... -

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Basic information

Entry
Database: PDB / ID: 5ol9
TitleStructure of human mitochondrial transcription elongation factor (TEFM) N-terminal domain
ComponentsTranscription elongation factor, mitochondrial
KeywordsTRANSCRIPTION / Elongation Factor / Mitochondria / Resolvase / RNA Polymerase
Function / homology
Function and homology information


transcription elongation by mitochondrial RNA polymerase / mitochondrial transcription / oxidative phosphorylation / DNA polymerase processivity factor activity / mitochondrial nucleoid / mitochondrial matrix / ribonucleoprotein complex / mitochondrion / RNA binding
Similarity search - Function
Transcription elongation factor, mitochondrial / Helix-hairpin-helix motif / RuvA domain 2-like / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ACETATE ION / Transcription elongation factor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.302 Å
AuthorsHillen, H.S. / Parshin, A.V. / Agaronyan, K. / Morozov, Y. / Graber, J.J. / Chernev, A. / Schwinghammer, K. / Urlaub, H. / Anikin, M. / Cramer, P. / Temiakov, D.
Funding support United States, Germany, 5items
OrganizationGrant numberCountry
National Institutes of HealthRO1GM104231 United States
German Research FoundationSFB860 Germany
European Research CouncilTRANSREGULON 693023 Germany
German Research FoundationSPP1935 Germany
Volkswagen Foundation Germany
CitationJournal: Cell / Year: 2017
Title: Mechanism of Transcription Anti-termination in Human Mitochondria.
Authors: Hillen, H.S. / Parshin, A.V. / Agaronyan, K. / Morozov, Y.I. / Graber, J.J. / Chernev, A. / Schwinghammer, K. / Urlaub, H. / Anikin, M. / Cramer, P. / Temiakov, D.
History
DepositionJul 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3002
Polymers12,2411
Non-polymers591
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area5180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.670, 47.670, 93.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transcription elongation factor, mitochondrial


Mass: 12240.936 Da / Num. of mol.: 1 / Fragment: UNP Residues 36-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEFM, C17orf42 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q96QE5
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: Sodium Acetate, Ammonium Acetate, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0, 2.0664
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.06641
ReflectionResolution: 1.3→42.46 Å / Num. obs: 27069 / % possible obs: 99.7 % / Redundancy: 25.05 % / CC1/2: 1 / Rmerge(I) obs: 0.105 / Net I/σ(I): 20.26
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 24.01 % / Rmerge(I) obs: 4.57 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1928 / CC1/2: 0.413 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.302→42.46 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.17
RfactorNum. reflection% reflection
Rfree0.1965 1354 5 %
Rwork0.1903 --
obs0.1906 27056 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.302→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 4 80 742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009717
X-RAY DIFFRACTIONf_angle_d0.946978
X-RAY DIFFRACTIONf_dihedral_angle_d14.345285
X-RAY DIFFRACTIONf_chiral_restr0.073111
X-RAY DIFFRACTIONf_plane_restr0.005128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3024-1.34890.4161320.37852494X-RAY DIFFRACTION98
1.3489-1.40290.37251320.35682512X-RAY DIFFRACTION99
1.4029-1.46680.35951310.33782494X-RAY DIFFRACTION100
1.4668-1.54410.26711340.26942532X-RAY DIFFRACTION100
1.5441-1.64090.26471350.23322562X-RAY DIFFRACTION100
1.6409-1.76760.26871330.21592537X-RAY DIFFRACTION100
1.7676-1.94550.17291350.1782560X-RAY DIFFRACTION100
1.9455-2.2270.17511360.16362593X-RAY DIFFRACTION100
2.227-2.80570.1531390.16532635X-RAY DIFFRACTION100
2.8057-42.48210.18181470.17422783X-RAY DIFFRACTION100
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)
15.42942.4594-2.59112.3966-0.05842.47620.06730.44610.4466-0.20390.05770.143-0.0435-0.1241-0.12570.2153-0.04520.01850.34290.0250.208843.374917.7657-1.0572
24.02560.482-1.30963.8528-2.94262.4726-0.11620.1917-0.2362-0.35380.16920.18760.5482-0.3377-0.04320.1543-0.0488-0.0120.19490.00220.183240.68098.57298.2354
33.05892.7409-2.33647.47572.60466.3610.2742-0.5538-0.41480.4354-0.3338-0.4589-0.01010.51360.22020.164-0.0164-0.01530.25480.05640.223346.94588.682722.153
43.54570.27670.61382.2699-0.41474.0122-0.0883-0.27920.08850.18750.04910.023-0.3585-0.23020.02890.1160.01020.01660.15920.01450.142843.73616.623218.444
56.68170.28624.4075.19271.81753.5592-0.32060.22030.1867-0.17010.2096-0.0068-1.05040.23990.03350.28080.0130.01670.20280.00950.18244.506323.132212.3612
64.2185-2.11390.05355.12640.40992.8313-0.0057-0.1003-0.3172-0.08850.0451-0.1454-0.24770.7351-0.05180.2028-0.09370.02080.42950.00710.224650.670313.02068.6005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 137 )

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