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- PDB-2xv4: Structure of Human RPC62 (partial) -

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Basic information

Entry
Database: PDB / ID: 2xv4
TitleStructure of Human RPC62 (partial)
ComponentsDNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3Polymerase
KeywordsTRANSCRIPTION / WINGED HELIX
Function / homology
Function and homology information


RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase III / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of innate immune response / RNA polymerase III complex ...RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase III / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of innate immune response / RNA polymerase III complex / positive regulation of interferon-beta production / DNA-directed 5'-3' RNA polymerase activity / single-stranded DNA binding / defense response to virus / innate immune response / DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
Helix Hairpins - #1450 / RNA polymerase III Rpc82, C -terminal / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Helix Hairpins - #1450 / RNA polymerase III Rpc82, C -terminal / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA-directed RNA polymerase III subunit RPC3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsLefevre, S. / Legrand, P. / Fribourg, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure-Function Analysis of Hrpc62 Provides Insights Into RNA Polymerase III Transcription
Authors: Lefevre, S. / Dumay-Odelot, H. / El Ayoubi, L. / Budd, A. / Legrand, P. / Pinaud, N. / Teichmann, M. / Fribourg, S.
History
DepositionOct 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9774
Polymers60,6931
Non-polymers2853
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.540, 69.920, 75.970
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3 / Polymerase / SHORT NAME=RNA POLYMERASE III SUBUNIT C3 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT C / RNA ...SHORT NAME=RNA POLYMERASE III SUBUNIT C3 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT C / RNA POLYMERASE III 62 KDA SUBUNIT / RPC62 / HRPC62


Mass: 60692.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD(DE3) PLYSS / References: UniProt: Q9BUI4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.82 Å3/Da / Density % sol: 0.56 % / Description: NONE
Crystal growpH: 7.5 / Details: BTP PH 7.5 GLYCEROL 10% PEG 3350 TACSIMATE 12%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.71
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71 Å / Relative weight: 1
ReflectionResolution: 2.95→43 Å / Num. obs: 16477 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 3.71 % / Biso Wilson estimate: 97.58 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.61
Reflection shellResolution: 2.95→3.07 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 3.53 / % possible all: 78.7

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.95→70.01 Å / Cor.coef. Fo:Fc: 0.8962 / Cor.coef. Fo:Fc free: 0.8967 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 846 5.07 %RANDOM
Rwork0.228 ---
obs0.2294 15653 --
Displacement parametersBiso mean: 104.18 Å2
Baniso -1Baniso -2Baniso -3
1-22.9365 Å20 Å2-15.5736 Å2
2--8.0533 Å20 Å2
3----30.9898 Å2
Refine analyzeLuzzati coordinate error obs: 0.502 Å
Refinement stepCycle: LAST / Resolution: 2.95→70.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 14 19 3217
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.164365HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1171SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes458HARMONIC5
X-RAY DIFFRACTIONt_it3236HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion20.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion441SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3790SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.15 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2673 148 4.93 %
Rwork0.2317 2853 -
all0.2334 3001 -

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