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- PDB-5aio: Crystal structure of t131 N-terminal TPR array -

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Basic information

Entry
Database: PDB / ID: 5aio
TitleCrystal structure of t131 N-terminal TPR array
ComponentsTRANSCRIPTION FACTOR TAU 131 KDA SUBUNIT
KeywordsTRANSCRIPTION / TFIIIC / TPRS
Function / homology
Function and homology information


5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor Tfc4/TFIIIC-102/Sfc4 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Transcription factor tau 131 kDa subunit
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.148 Å
AuthorsMale, G. / Glatt, S. / Mueller, C.W.
CitationJournal: Nat Commun / Year: 2015
Title: Architecture of TFIIIC and its role in RNA polymerase III pre-initiation complex assembly.
Authors: Male, G. / von Appen, A. / Glatt, S. / Taylor, N.M. / Cristovao, M. / Groetsch, H. / Beck, M. / Muller, C.W.
History
DepositionFeb 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 2.0Feb 14, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 2.1May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
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: TRANSCRIPTION FACTOR TAU 131 KDA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)52,4381
Polymers52,4381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.360, 116.360, 95.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein TRANSCRIPTION FACTOR TAU 131 KDA SUBUNIT / TFIIIC 131 KDA SUBUNIT / TRANSCRIPTION FACTOR C SUBUNIT 4


Mass: 52437.973 Da / Num. of mol.: 1 / Fragment: T131 N-TERMINAL TPR ARRAY, RESIDUES 123-566
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P33339

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.61 % / Description: NONE
Crystal growDetails: 0.2 M MGCL2, 0.1 M TRIS PH 8.3 AND 42.5% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 12884 / % possible obs: 99.9 % / Observed criterion σ(I): 1.7 / Redundancy: 39.3 % / Biso Wilson estimate: 134.95 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 38.3 % / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.148→44.612 Å / SU ML: 0.69 / σ(F): 1.36 / Phase error: 39.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 643 5 %
Rwork0.25 --
obs0.2519 12884 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.148→44.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 0 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043517
X-RAY DIFFRACTIONf_angle_d0.7134761
X-RAY DIFFRACTIONf_dihedral_angle_d13.5031302
X-RAY DIFFRACTIONf_chiral_restr0.031518
X-RAY DIFFRACTIONf_plane_restr0.002612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1482-3.39120.43941270.40032425X-RAY DIFFRACTION100
3.3912-3.73230.35961280.35282438X-RAY DIFFRACTION100
3.7323-4.2720.32081270.30742435X-RAY DIFFRACTION100
4.272-5.38090.33681290.2712450X-RAY DIFFRACTION100
5.3809-44.61630.22841320.19682493X-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)
12.14370.08510.62854.835-2.62483.50060.8976-1.2553-0.02051.8925-0.8871-0.9445-0.60681.6283-0.11072.1518-0.4413-0.48881.82980.41231.4612-29.354114.452357.9157
24.33832.8451-5.66246.0953-5.85888.40181.4822-0.76280.15082.2744-0.61250.1077-1.29490.6466-0.89271.6439-0.4198-0.26351.05450.01341.3652-29.4831.85825.3051
36.98263.558-0.39657.43431.44143.5317-0.46740.8522-0.1855-0.33610.6065-0.24520.763-0.0797-0.07650.9047-0.1633-0.11.0158-0.06421.0414-23.652428.3725-5.3616
46.43243.7845-1.28698.1456-5.0144.58040.4278-0.70990.02220.9872-0.55181.432-0.94831.19670.20571.7695-0.49250.23151.6823-0.38651.9971-47.892-0.6251-10.3595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 131 THROUGH 175 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 176 THROUGH 314 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 315 THROUGH 514 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 515 THROUGH 565 )

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