[English] 日本語
Yorodumi
- PDB-1jfi: Crystal Structure of the NC2-TBP-DNA Ternary Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jfi
TitleCrystal Structure of the NC2-TBP-DNA Ternary Complex
Components
  • (Transcription Regulator NC2 ...) x 2
  • 5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP*C)-3'
  • TATA-BOX-BINDING PROTEIN (TBP)
KeywordsTRANSCRIPTION/DNA / Histone / H2A/H2B / TBP / TATA-DNA / transcription initiation / NC2 / Negative Cofactor / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


negative cofactor 2 complex / : / : / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / Signaling by Activin / 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 ...negative cofactor 2 complex / : / : / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / Signaling by Activin / 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 / Signaling by NODAL / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / 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 / RNA polymerase II transcription regulator complex / transcription corepressor activity / HATs acetylate histones / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Negative cofactor 2 complex subunit beta / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / TATA-Binding Protein / 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. ...Negative cofactor 2 complex subunit beta / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / TATA-Binding Protein / 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. / Histone, subunit A / Histone, subunit A / TBP domain superfamily / Histone-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Protein Dr1 / Dr1-associated corepressor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKamada, K. / Shu, F. / Chen, H. / Malik, S. / Stelzer, G. / Roeder, R.G. / Meisterernst, M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.
Authors: Kamada, K. / Shu, F. / Chen, H. / Malik, S. / Stelzer, G. / Roeder, R.G. / Meisterernst, M. / Burley, S.K.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: 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 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: 5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP*C)-3'
E: 5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP*A)-3'
A: Transcription Regulator NC2 alpha chain
B: Transcription Regulator NC2 beta chain
C: TATA-BOX-BINDING PROTEIN (TBP)


Theoretical massNumber of molelcules
Total (without water)63,0765
Polymers63,0765
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.684, 119.075, 155.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
DNA chain , 2 types, 2 molecules DE

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


Mass: 5844.796 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 19 BASE-PAIR TATA-CONTAINING OLIGONUCLEOTIDE TOP STRAND
#2: DNA chain 5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP*A)-3'


Mass: 5804.773 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 19 BASE-PAIR TATA-CONTAINING OLIGONUCLEOTIDE BOTTOM STRAND

-
Transcription Regulator NC2 ... , 2 types, 2 molecules AB

#3: Protein Transcription Regulator NC2 alpha chain


Mass: 10813.676 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NC2 alpha (DRAP1)
Plasmid details: His tag eliminated. coexpressed with NC2 beta
Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14919
#4: Protein Transcription Regulator NC2 beta chain / DR1 PROTEIN


Mass: 19755.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NC2 beta (Dr1) / Plasmid details: coexpressed with NC2 alpha / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01658

-
Protein / Non-polymers , 2 types, 10 molecules C

#5: Protein TATA-BOX-BINDING PROTEIN (TBP) / Transcription Initiation Factor TFIID


Mass: 20856.729 Da / Num. of mol.: 1 / Fragment: RESIDUES 359-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: tbp / Plasmid details: codon usage is optimized for this gene / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20226
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium citrate11
3KCl11
4MgCl211
5DTT11
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMprotein1drop
2100 mM1reservoir
3100 mM1reservoirKCl
420 mM1reservoirMgCl2
510 mMdithiothreitol1reservoir
620 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.984
DetectorType: SBC-2 / Detector: CCD / Date: Jul 2, 2000 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.62→20 Å / Num. all: 21406 / Num. obs: 21406 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 78.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 19.6
Reflection shellResolution: 2.62→2.71 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.312 / Num. unique all: 1952 / Rsym value: 0.312 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 562756

-
Processing

Software
NameVersionClassificationNB
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDW

1cdw


Resolution: 2.62→19.84 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1499 7.1 %RANDOM
Rwork0.233 ---
all0.239 21653 --
obs0.236 21084 97.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 29.7687 Å2 / ksol: 0.302265 e/Å3
Displacement parametersBiso mean: 61.53 Å2
Baniso -1Baniso -2Baniso -3
1--16.66 Å20 Å20 Å2
2--21.02 Å20 Å2
3----4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.62→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 732 0 9 3743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.62-2.740.3531776.70.3623870.02790.1
2.74-2.880.3291927.20.33325720.02496.1
2.88-3.060.2811736.50.28326220.02197.8
3.06-3.30.2951937.20.29426270.02198.3
3.3-3.630.2551786.60.25226670.01999
3.63-4.150.2251866.90.22226970.01699.4
4.15-5.210.1792017.40.17927190.01399.7
5.21-19.840.20719970.20827930.01598.4
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 7.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.353 / % reflection Rfree: 6.7 % / Rfactor Rwork: 0.36

+
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