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- PDB-2j04: The tau60-tau91 subcomplex of yeast transcription factor IIIC -

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Basic information

Entry
Database: PDB / ID: 2j04
TitleThe tau60-tau91 subcomplex of yeast transcription factor IIIC
Components
  • HYPOTHETICAL PROTEIN YPL007CHypothesis
  • YDR362CP
KeywordsTRANSCRIPTION / BETA PROPELLER / TYPE 2 PROMOTERS / HYPOTHETICAL PROTEIN / PREINITIATION COMPLEX / YEAST RNA POLYMERASE III / TRANSCRIPTION FACTOR IIIC
Function / homology
Function and homology information


: / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / transcription by RNA polymerase III / DNA binding / nucleus
Similarity search - Function
Transcription factor IIIC, putative zinc-finger / Putative zinc-finger of transcription factor IIIC complex / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Transcription factor tau 91 kDa subunit / Transcription factor tau 60 kDa subunit
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsMylona, A. / Fernandez-Tornero, C. / Legrand, P. / Muller, C.W.
CitationJournal: Mol.Cell / Year: 2006
Title: Structure of the Tau60/Deltatau91 Subcomplex of Yeast Transcription Factor Iiic: Insights Into Preinitiation Complex Assembly
Authors: Mylona, A. / Fernandez-Tornero, C. / Legrand, P. / Haupt, M. / Sentenac, A. / Acker, J. / Muller, C.W.
History
DepositionJul 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN YPL007C
B: YDR362CP
C: HYPOTHETICAL PROTEIN YPL007C
D: YDR362CP


Theoretical massNumber of molelcules
Total (without water)253,3684
Polymers253,3684
Non-polymers00
Water905
1
A: HYPOTHETICAL PROTEIN YPL007C
B: YDR362CP


Theoretical massNumber of molelcules
Total (without water)126,6842
Polymers126,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: HYPOTHETICAL PROTEIN YPL007C
D: YDR362CP


Theoretical massNumber of molelcules
Total (without water)126,6842
Polymers126,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.420, 125.800, 210.470
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C
14B
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 399
2111C2 - 399
1126A400 - 408
2126C400 - 408
1131A409 - 486
2131C409 - 486
1235A487 - 504
2235C487 - 504
1331A505 - 535
2331C505 - 535
1431A543 - 567
2431C543 - 567
1532A568 - 587
2532C568 - 587
1141B1 - 999
2141D1 - 999

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.41877, 0.8599, -0.29189), (0.83544, 0.23884, -0.49496), (-0.3559, -0.45114, -0.81842)61.74368, 37.25398, 216.04717
2given(-0.4162, 0.85779, -0.30161), (0.85668, 0.25875, -0.44626), (-0.30476, -0.44412, -0.84255)62.3139, 34.0905, 216.59775

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Components

#1: Protein HYPOTHETICAL PROTEIN YPL007C / Hypothesis / TAU60 / YPL007P


Mass: 67755.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PVL1393 / Cell line (production host): High Five / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q12308
#2: Protein YDR362CP / TAU91


Mass: 58928.871 Da / Num. of mol.: 2 / Fragment: PROPELLER DOMAIN, RESIDUES 159-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET-28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q06339
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLONING ARTIFACT C-TERMINAL NON-CLEVABLE HIS- TAG

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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: 3.42 Å3/Da / Density % sol: 63.74 %
Crystal growpH: 7 / Details: 0.8 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 49476 / % possible obs: 98.6 % / Observed criterion σ(I): 1.8 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→208.51 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.882 / SU B: 54.87 / SU ML: 0.409 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2619 5 %RANDOM
Rwork0.212 ---
obs0.214 49476 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-5 Å2
2--0.35 Å20 Å2
3----4.37 Å2
Refinement stepCycle: LAST / Resolution: 3.2→208.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16930 0 0 5 16935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02217323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.94123510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.79452100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7224.53777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.497153014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2111570
X-RAY DIFFRACTIONr_chiral_restr0.1250.22664
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2730.28682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.211753
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2529
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1971.510760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.314217171
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39437464
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6084.56339
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3232tight positional0.050.05
3A1157tight positional0.080.05
4B3677tight positional0.040.05
3A152medium positional0.460.3
2A73loose positional0.521.2
3A74loose positional1.361.2
1A3232tight thermal0.010.15
3A1157tight thermal0.010.15
4B3677tight thermal00.15
3A152medium thermal0.110.5
2A73loose thermal0.992
3A74loose thermal0.932
LS refinement shellResolution: 3.2→3.34 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.371 310
Rwork0.314 5905
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)
13.22880.79760.99783.34541.95045.403-0.2235-0.450.35290.0881-0.08270.1354-0.0676-0.26680.3061-0.5237-0.00550.064-0.0967-0.0249-0.209312.139717.475444.5235
25.8112-1.7377-2.53832.52370.74695.29330.02740.02230.0463-0.1611-0.07020.1882-0.0068-0.26120.0428-0.4877-0.058-0.032-0.7356-0.0383-0.313215.513412.19115.9418
31.5327-0.4505-0.01352.345-0.4167.44140.04290.6828-0.1993-0.1481-0.1319-0.04190.18160.40990.0889-0.1113-0.0844-0.1216-0.3039-0.0837-0.081558.75629.6001167.6044
43.00721.92440.58118.9142.42782.6392-0.008-0.03750.1991-0.51-0.13420.7807-0.0417-0.37190.1421-0.4415-0.02350.0316-0.58990.0768-0.32463.949450.1267199.6204
51.65720.28291.53461.1793-0.04516.5954-0.1343-0.12850.14780.2838-0.0251-0.0990.3617-0.2390.1594-0.29860.00070.078-0.0135-0.2226-0.164529.251119.740682.8881
61.74190.1922.11861.54980.77196.30310.1050.2829-0.03930.1379-0.1881-0.03660.2935-0.17230.0831-0.0752-0.06030.039-0.0323-0.1632-0.206541.99427.016129.0657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 402
2X-RAY DIFFRACTION2A403 - 588
3X-RAY DIFFRACTION3C3 - 402
4X-RAY DIFFRACTION4C403 - 588
5X-RAY DIFFRACTION5B165 - 675
6X-RAY DIFFRACTION6D167 - 675

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