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- PDB-2j49: Crystal structure of yeast TAF5 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2j49
TitleCrystal structure of yeast TAF5 N-terminal domain
ComponentsTRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5
KeywordsTRANSCRIPTION / NUCLEAR PROTEIN / TRANSCRIPTION REGULATION / TAF5 / TFIID / WD REPEAT / INITIATION
Function / homology
Function and homology information


SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity ...SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / ubiquitin binding / transcription initiation at RNA polymerase II promoter / chromatin organization / transcription by RNA polymerase II / molecular adaptor activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
TFIID subunit TAF5, NTD2 domain / LisH / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...TFIID subunit TAF5, NTD2 domain / LisH / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsRomier, C. / James, N. / Birck, C. / Cavarelli, J. / Vivares, C. / Collart, M.A. / Moras, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure, Biochemical and Genetic Characterization of Yeast and E. Cuniculi Taf(II)5 N-Terminal Domain: Implications for TFIID Assembly.
Authors: Romier, C. / James, N. / Birck, C. / Cavarelli, J. / Vivares, C. / Collart, M.A. / Moras, D.
History
DepositionAug 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5


Theoretical massNumber of molelcules
Total (without water)17,2831
Polymers17,2831
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.340, 91.340, 55.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 5 / TBP-ASSOCIATED FACTOR 5 / TBP-ASSOCIATED FACTOR 90 KDA / TAFII-90


Mass: 17282.674 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 147-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38129
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 4 RESIDUES REPRESENT THE THROMBIN CUTTING SITE (GS) AND THE NDEL CLONING SITE (HM) AND ...THE FIRST 4 RESIDUES REPRESENT THE THROMBIN CUTTING SITE (GS) AND THE NDEL CLONING SITE (HM) AND ARE NOT PART OF THE FULL PROTEIN. THESE RESIDUES ARE MAPPED TO THE PDB ENTRY.

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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: 2.75 Å3/Da / Density % sol: 54.88 %
Crystal growpH: 6.5 / Details: 0.05 M CACODYLATE PH 6.5,2.4 M NA FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.973178
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973178 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 7594 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 42
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.7 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SOLOMONphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→45.64 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 17.315 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 807 10.6 %RANDOM
Rwork0.215 ---
obs0.221 6781 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20.74 Å20 Å2
2--1.48 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 0 37 1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9471552
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2615133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30523.79358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96615197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.441156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02870
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2529
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2804
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5721.5695
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92621096
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2533519
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.864.5456
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
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 55
Rwork0.245 509
Refinement TLS params.Method: refined / Origin x: 28.575 Å / Origin y: 32.52 Å / Origin z: 54.171 Å
111213212223313233
T-0.4535 Å20.0249 Å20.0337 Å2--0.4416 Å2-0.0202 Å2---0.1024 Å2
L6.7694 °21.6449 °21.2123 °2-4.3537 °20.1752 °2--5.2113 °2
S-0.3166 Å °-0.0433 Å °0.3952 Å °-0.1427 Å °0.3348 Å °-0.2129 Å °-0.2731 Å °-0.2711 Å °-0.0182 Å °

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