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- PDB-1nvp: HUMAN TFIIA/TBP/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1nvp
TitleHUMAN TFIIA/TBP/DNA COMPLEX
Components
  • (Transcription initiation factor IIA ...) x 3
  • 5'-D(*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*CP*CP*CP*C)-3'
  • 5'-D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3'
  • TATA box binding proteinTATA-binding protein
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA / COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / 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 / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus ...RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / 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 / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 I Transcription Initiation / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / transcription by RNA polymerase III / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / cell junction / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Helix Hairpins - #100 / TATA-Binding Protein / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain ...Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Helix Hairpins - #100 / TATA-Binding Protein / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / Helix Hairpins / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBleichenbacher, M. / Tan, S. / Richmond, T.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes.
Authors: Bleichenbacher, M. / Tan, S. / Richmond, T.J.
History
DepositionFeb 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3'
F: 5'-D(*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*CP*CP*CP*C)-3'
A: TATA box binding protein
B: Transcription initiation factor IIA alpha chain
C: Transcription initiation factor IIA beta chain
D: Transcription initiation factor IIA gamma chain


Theoretical massNumber of molelcules
Total (without water)58,3716
Polymers58,3716
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.624, 90.884, 125.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules EF

#1: DNA chain 5'-D(*GP*GP*GP*GP*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*G)-3'


Mass: 5381.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*CP*CP*CP*C)-3'


Mass: 5034.261 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Transcription initiation factor IIA ... , 3 types, 3 molecules BCD

#4: Protein Transcription initiation factor IIA alpha chain / TFIIA p35 and p19 subunits / TFIIA-42 / TFIIAL


Mass: 6486.258 Da / Num. of mol.: 1 / Fragment: N-terminal 58 amino acids
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1 OR TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52655
#5: Protein Transcription initiation factor IIA beta chain / TFIIA p35 and p19 subunits / TFIIA-42 / TFIIAL


Mass: 8687.350 Da / Num. of mol.: 1 / Fragment: c-terminal 76 amino acids
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1 OR TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52655
#6: Protein Transcription initiation factor IIA gamma chain / TFIIA P12 subunit / TFIIA-12 / TFIIAS / TFIIA-gamma


Mass: 12337.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2 OR TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657

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Protein / Non-polymers , 2 types, 232 molecules A

#3: Protein TATA box binding protein / TATA-binding protein / Transcription initiation factor TFIID / TATA-box factor / TATA sequence-binding protein / TBP


Mass: 20443.254 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 181 AMINO ACIDS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP OR TFIID OR TF2D / Production host: Escherichia coli (E. coli) / References: UniProt: P20226
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, lithium nitrate, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2lithium nitrate11
3CaCl211
4CaCl212
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
22 mMBis-Tris1droppH7.0
320 mM1dropKCl
40.1 mMEDTA1drop
50.5 mMdithiothreitol1drop
60.01 %(w/v)1dropNaN3
750 mMbis-Tris1reservoirpH6.5
8100 mM1reservoirLiNO3
910 mM1reservoirCaCl2
101 mMdithiothreitol1reservoir
1112 %(w/v)PEG60001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1110.916, 0.909
ROTATING ANODERIGAKU RU20021.54
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMar 21, 1997
MARRESEARCH2IMAGE PLATEDec 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9161
20.9091
31.541
ReflectionResolution: 2.1→39 Å / Num. obs: 40386 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Redundancy: 5.6 % / Num. measured all: 224980
Reflection shell
*PLUS
% possible obs: 99.8 % / Redundancy: 3.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINED ALSO WITH REFMAC BY MURSHUDOV, VAGIN, DODSON. NO ELECTRON DENSITY VISIBLE FOR: RESIDUES 339, CHAIN A RESIDUES 2-8, CHAIN B RESIDUES 52-58, CHAIN B RESIDUES 301-329, CHAIN C RESIDUE ...Details: REFINED ALSO WITH REFMAC BY MURSHUDOV, VAGIN, DODSON. NO ELECTRON DENSITY VISIBLE FOR: RESIDUES 339, CHAIN A RESIDUES 2-8, CHAIN B RESIDUES 52-58, CHAIN B RESIDUES 301-329, CHAIN C RESIDUE 2, CHAIN D RESIDUES 100-109, CHAIN D SIDE CHAINS FOR RESIDUES K12 OF CHAIN B. SIDE CHAINS FOR RESIDUES D330, R363 OF CHAIN C. SIDE CHAINS FOR RESIDUES Q50, R51, R53, T85, Q86 OF CHAIN D.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3268 8.1 %RANDOM
Rwork0.229 ---
obs0.229 40386 99.6 %-
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å20 Å2
2---10.15 Å20 Å2
3---12.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 691 0 231 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.362
X-RAY DIFFRACTIONc_mcangle_it3.513
X-RAY DIFFRACTIONc_scbond_it6.184
X-RAY DIFFRACTIONc_scangle_it8.486
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 519 7.9 %
Rwork0.29 6060 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / Rfactor Rwork: 0.29

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