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- PDB-5afq: Crystal structure of RPC62 - RPC32 beta -

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Basic information

Entry
Database: PDB / ID: 5afq
TitleCrystal structure of RPC62 - RPC32 beta
Components
  • DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
  • RPC32 BETA (RPC7L)
KeywordsREPLICATION / HUMAN RNA POLYMERASE III
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
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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase III subunit RPC3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsFribourg, S.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural Analysis of Human Rpc32Beta - Rpc62 Complex.
Authors: Boissier, F. / Dumay-Odelot, H. / Teichmann, M. / Fribourg, S.
History
DepositionJan 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
B: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
D: RPC32 BETA (RPC7L)
E: RPC32 BETA (RPC7L)


Theoretical massNumber of molelcules
Total (without water)158,5274
Polymers158,5274
Non-polymers00
Water00
1
A: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
D: RPC32 BETA (RPC7L)


Theoretical massNumber of molelcules
Total (without water)79,2632
Polymers79,2632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-18.7 kcal/mol
Surface area26010 Å2
MethodPISA
2
B: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
E: RPC32 BETA (RPC7L)


Theoretical massNumber of molelcules
Total (without water)79,2632
Polymers79,2632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-6.4 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.270, 218.270, 182.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3 / RNA POLYMERASE III SUBUNIT C3 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT C / RNA POLYMERASE III 62 ...RNA POLYMERASE III SUBUNIT C3 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT C / RNA POLYMERASE III 62 KDA SUBUNIT / RPC62 / RPC62


Mass: 60692.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9BUI4
#2: Protein RPC32 BETA (RPC7L)


Mass: 18570.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
Sequence detailsCHAIN D AND E IS RPC32 BETA (RPC7L), FRAGMENT 50-134 EXPRESSED AS RPC62 IN ROSETTA (DE3) STRAINS ...CHAIN D AND E IS RPC32 BETA (RPC7L), FRAGMENT 50-134 EXPRESSED AS RPC62 IN ROSETTA (DE3) STRAINS FROM E. COLI. SINCE THE REGISTER OF THE AMINO ACIDS ARE NOT KNOWN, CHAINS D AND E HAS BEEN BUILT IN AS UNK IN THE MODEL.

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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: 3.89 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7.5 / Details: 100MM ADA PH 6.5, 100MM LI2SO4, 14% PEG 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 7→86 Å / Num. obs: 3668 / % possible obs: 99.2 % / Observed criterion σ(I): 1.2 / Redundancy: 4.9 % / Biso Wilson estimate: 444.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.1
Reflection shellResolution: 7→7.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XUB

2xub


Resolution: 7→30.75 Å / Cor.coef. Fo:Fc: 0.8629 / Cor.coef. Fo:Fc free: 0.8427 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 2.972
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 342 9.5 %RANDOM
Rwork0.2678 ---
obs0.2708 3612 99.15 %-
Displacement parametersBiso mean: 300 Å2
Baniso -1Baniso -2Baniso -3
1-12.0094 Å20 Å20 Å2
2--12.0094 Å20 Å2
3----24.0188 Å2
Refinement stepCycle: LAST / Resolution: 7→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7387 0 0 0 7387
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d7478HARMONIC2
X-RAY DIFFRACTIONt_angle_deg10098HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2684SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes194HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1084HARMONIC5
X-RAY DIFFRACTIONt_it7478HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1035SEMIHARMONIC5
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_contact9587SEMIHARMONIC4
LS refinement shellResolution: 7→7.83 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3198 98 9.82 %
Rwork0.2797 900 -
all0.2836 998 -
obs--99.15 %

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