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- PDB-3spa: Crystal Structure of Human Mitochondrial RNA Polymerase -

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Basic information

Entry
Database: PDB / ID: 3spa
TitleCrystal Structure of Human Mitochondrial RNA Polymerase
Components
  • DNA-directed RNA polymerase, mitochondrial
  • Nonamer peptide
KeywordsTRANSFERASE / single-subunit DNA-dependent RNA Polymerase in mitochondria / Mitochondria
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / transcription initiation at mitochondrial promoter / Strand-asynchronous mitochondrial DNA replication / mitochondrial transcription / : / mitochondrial nucleoid / : / DNA-directed RNA polymerase activity ...Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / transcription initiation at mitochondrial promoter / Strand-asynchronous mitochondrial DNA replication / mitochondrial transcription / : / mitochondrial nucleoid / : / DNA-directed RNA polymerase activity / Transcriptional activation of mitochondrial biogenesis / : / : / : / : / : / : / DNA-directed RNA polymerase / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / mitochondrial matrix / protein-containing complex / mitochondrion / RNA binding
Similarity search - Function
DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Tetratricopeptide-like helical domain superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRingel, R. / Sologub, M. / Morozov, Y.I. / Litonin, D. / Cramer, P. / Temiakov, D.
CitationJournal: Nature / Year: 2011
Title: Structure of human mitochondrial RNA polymerase
Authors: Ringel, R. / Sologub, M. / Morozov, Y.I. / Litonin, D. / Cramer, P. / Temiakov, D.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999THE AUTHOR STATES THAT CHAINS B IS LIKELY PARTS OF THE N-TERMINI OF CHAINS A. DUD TO DISORDER, IT ...THE AUTHOR STATES THAT CHAINS B IS LIKELY PARTS OF THE N-TERMINI OF CHAINS A. DUD TO DISORDER, IT WAS NOT POSSIBLE TO ACCURATELY ASSIGN THE SIDE CHAINS AND IDENTIFY THE PEPTIDES. SO THEY ARE MODELED AS UNK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase, mitochondrial
B: Nonamer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,97810
Polymers129,5202
Non-polymers4588
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-58 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.258, 211.258, 60.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein DNA-directed RNA polymerase, mitochondrial / MtRPOL


Mass: 128736.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAC06147.1, POLRMT / Plasmid: pProExHtb / Production host: Escherichia coli (E. coli) / References: UniProt: O00411, DNA-directed RNA polymerase
#2: Protein/peptide Nonamer peptide


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAC06147.1, POLRMT / Plasmid: pProExHtb / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 153 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG4000, 10% Glycerol, 30mM Mes 6.5, 60mM (NH4)2SO4, 40mM Tris 8.0, 20mM DTT in situ proteolysed with ArgC (1:1000 w/w ratio) and micro-seeded, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 63 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→58.128 Å / Num. all: 46595 / Num. obs: 46507 / Redundancy: 3.8 % / Biso Wilson estimate: 73.16 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6694

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QLN, truncated to polyAlanine, residues 246-354, 392-568, 691-741, 766-883 of model used

1qln


Resolution: 2.5→58.128 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9259 / SU R Cruickshank DPI: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 326-360 were refined with correct sequence and afterwards rebuild to poly Alanine because of poor side chain density and possible sequence shifts in this region. PDB includes these ...Details: Residues 326-360 were refined with correct sequence and afterwards rebuild to poly Alanine because of poor side chain density and possible sequence shifts in this region. PDB includes these residues as UNK. An unconnected helix is build as poly Alanine and also named with UNK residues in the PDB. Residues 1002-1005 possibly have more conformations than built, explaining additional positive density.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2378 5.11 %RANDOM
Rwork0.1855 ---
all0.1878 46507 --
obs0.1878 46505 99.81 %-
Displacement parametersBiso mean: 89.21 Å2
Baniso -1Baniso -2Baniso -3
1-9.3566 Å20 Å20 Å2
2--9.3566 Å20 Å2
3----18.7131 Å2
Refine analyzeLuzzati coordinate error obs: 0.387 Å
Refinement stepCycle: LAST / Resolution: 2.5→58.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7457 0 22 145 7624
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONo_bond_d0.0097788HARMONIC2
X-RAY DIFFRACTIONo_angle_deg1.1210572HARMONIC2
X-RAY DIFFRACTIONo_dihedral_angle_d2730SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes175HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1134HARMONIC5
X-RAY DIFFRACTIONt_it7788HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion19.41
X-RAY DIFFRACTIONt_chiral_improper_torsion965SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8928SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2775 160 4.74 %
Rwork0.2372 3215 -
all0.239 3375 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 3.3823 Å / Origin y: 41.4659 Å / Origin z: -0.7464 Å
111213212223313233
T-0.1615 Å2-0.0184 Å2-0.0666 Å2--0.2771 Å2-0.0595 Å2---0.075 Å2
L1.221 °20.4029 °20.1228 °2-1.8714 °20.0422 °2--0.4206 °2
S0.0106 Å °0.0802 Å °-0.1549 Å °-0.2354 Å °0.0117 Å °0.3595 Å °0.0873 Å °-0.0767 Å °-0.0223 Å °
Refinement TLS groupSelection details: { A|* }

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