[English] 日本語
Yorodumi
- PDB-1qn8: Crystal structure of the T(-28) Adenovirus major late promoter TA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qn8
TitleCrystal structure of the T(-28) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')
  • TRANSCRIPTION INITIATION FACTOR TFIID-1
KeywordsTATA BOX-BINDING PROTEIN (TBP) / ADENOVIRUS MAJOR LATE PROMOTER (ADMLP) TATA BOX / TBP-TATA ELEMENT COMPLEXES / T (- 28) TATA BOX VARIANT
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA binding / nucleus
Similarity search - Function
TATA-Binding Protein / TATA-Binding Protein / TATA-box binding protein, eukaryotic / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein 1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsPatikoglou, G.A. / Kim, J.L. / Sun, L. / Yang, S.-H. / Kodadek, T. / Burley, S.K.
CitationJournal: Genes Dev. / Year: 1999
Title: TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution
Authors: Patikoglou, G.A. / Kim, J.L. / Sun, L. / Yang, S.-H. / Kodadek, T. / Burley, S.K.
History
DepositionOct 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR TFIID-1
B: TRANSCRIPTION INITIATION FACTOR TFIID-1
C: DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')
E: DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)61,9206
Polymers61,9206
Non-polymers00
Water6,287349
1
A: TRANSCRIPTION INITIATION FACTOR TFIID-1
C: DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,9603
Polymers30,9603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-9.6 kcal/mol
Surface area14840 Å2
MethodPQS
2
B: TRANSCRIPTION INITIATION FACTOR TFIID-1
E: DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,9603
Polymers30,9603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-9.8 kcal/mol
Surface area15340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)41.800, 146.700, 57.400
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00172, -0.00289), (0.00176, -0.99989, 0.01462), (-0.00287, -0.01463, -0.99989)
Vector: 8.99841, -88.3204, 217.52924)

-
Components

#1: Protein TRANSCRIPTION INITIATION FACTOR TFIID-1 / TATA-BOX FACTOR 1 / TATA SEQUENCE-BINDING PROTEIN 1 / TBP1


Mass: 22400.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P28147
#2: DNA chain DNA (5'-D(*GP*CP*TP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*A)-3')


Mass: 4328.841 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*TP*AP*GP*C)-3')


Mass: 4230.765 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDNA MOLECULES BOUND WITHIN THE SERIES CHAIN C, E CHAIN D, F 1QN3 GCTATAAACGGGCA TGCCCGTTTATAGC 1QN4 ...DNA MOLECULES BOUND WITHIN THE SERIES CHAIN C, E CHAIN D, F 1QN3 GCTATAAACGGGCA TGCCCGTTTATAGC 1QN4 GCTATAAAATGGCA TGCCATTTTATAGC 1QN5 GCTATAAGAGGGCA TGCCCTCTTATAGC 1QN6 GCTATAATAGGGCA TGCCCTATTATAGC 1QN7 GCTATATAAGGGCA TGCCCTTATATAGC 1QN8 GCTATTAAAGGGCA TGCCCTTTAATAGC 1QN9 GCTACAAAAGGGCA TGCCCTTTTGTAGC 1QNA GCTTTAAAAGGGCA TGCCCTTTTAAAGC 1QNB GCTATAAATGGGCA TGCCCATTTATAGC 1QNC GCAATAAAAGGGCA TGCCCTTTTATTGC 1QNE GCTATAAAAGGGCA TGCCCTTTTATAGC

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMcomplex1drop
240 mMMES1drop
360 mM1dropor 100 mMKCl
414 %(v/v)glycerol1drop
54 mM1dropMgCl2
6300 mMammonium acetate1drop
710 mMdithiothreitol1drop
812 %(v/v)glycerol1reservoir
925 mMMES1reservoir
1010 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.09→15 Å / Num. obs: 40252 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.045
Reflection
*PLUS
Rmerge(I) obs: 0.045

-
Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.1→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3284 10 %RANDOM
Rwork0.194 ---
obs0.194 36307 97 %-
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 1134 0 349 4399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more