[English] 日本語
Yorodumi
- PDB-1c9b: CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c9b
TitleCRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP)
Components
  • (ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT) x 2
  • GENERAL TRANSCRIPTION FACTOR IIB
  • TATA BOX BINDING PROTEIN
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / CYCLIN-LIKE FOLD / HELIX-TURN-HELIX / TATA-BOX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of core promoter binding / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / meiotic sister chromatid cohesion / RNA polymerase III general transcription initiation factor activity / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / 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 ...positive regulation of core promoter binding / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / meiotic sister chromatid cohesion / RNA polymerase III general transcription initiation factor activity / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / 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 / transcription factor TFIIA complex / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus / female pronucleus / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / RNA polymerase II general transcription initiation factor activity / protein acetylation / transcription factor TFIID complex / cell division site / acetyltransferase activity / 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 / aryl hydrocarbon receptor binding / RNA polymerase II complex binding / viral transcription / TFIIB-class transcription factor binding / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / spindle 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 / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / euchromatin / protein-DNA complex / NoRC negatively regulates rRNA expression / kinetochore / B-WICH complex positively regulates rRNA expression / RNA polymerase II transcription regulator complex / chromosome / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / Estrogen-dependent gene expression / DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding ...TATA-Binding Protein / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / 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. / Cyclin A; domain 1 / TBP domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsTsai, F.T.F. / Sigler, P.B.
Citation
Journal: EMBO J. / Year: 2000
Title: Structural basis of preinitiation complex assembly on human pol II promoters.
Authors: Tsai, F.T. / Sigler, P.B.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The structural basis for the oriented assembly of a TBP/TFB/promoter complex
Authors: Littlefield, O. / Korkhin, Y. / Sigler, P.B.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1998
Title: Polarity of transcription on Pol II and archaeal promoters: where is the "one- way sign" and how is it read?
Authors: Tsai, F.T.F. / Littlefield, O. / Kosa, P.F. / Cox, J.M. / Schepartz, A. / Sigler, P.B.
#3: Journal: Nature / Year: 1995
Title: Crystal structure of a TFIIB-TBP-TATA-element ternary complex
Authors: Nikolov, D.B. / Chen, H. / Halay, E.D. / Usheva, A.A. / Hisatake, K. / Lee, D.K. / Roeder, R.G. / Burley, S.K.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box- binding protein/ transcription factor (II) B core/TATA-box
Authors: Kosa, P.F. / Ghosh, G. / DeDecker, B. / Sigler, P.B.
#5: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein
Authors: Bagby, S. / Kim, S. / Maldonado, E. / Tong, K.I. / Reinberg, D. / Ikura, M.
History
DepositionAug 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
D: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
G: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
H: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
K: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
L: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
O: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
P: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
S: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
T: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
A: GENERAL TRANSCRIPTION FACTOR IIB
B: TATA BOX BINDING PROTEIN
E: GENERAL TRANSCRIPTION FACTOR IIB
F: TATA BOX BINDING PROTEIN
I: GENERAL TRANSCRIPTION FACTOR IIB
J: TATA BOX BINDING PROTEIN
M: GENERAL TRANSCRIPTION FACTOR IIB
N: TATA BOX BINDING PROTEIN
Q: GENERAL TRANSCRIPTION FACTOR IIB
R: TATA BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)272,21620
Polymers272,21620
Non-polymers00
Water5,927329
1
C: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
D: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
A: GENERAL TRANSCRIPTION FACTOR IIB
B: TATA BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,4434
Polymers54,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
H: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
E: GENERAL TRANSCRIPTION FACTOR IIB
F: TATA BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,4434
Polymers54,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
L: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
I: GENERAL TRANSCRIPTION FACTOR IIB
J: TATA BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,4434
Polymers54,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
P: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
M: GENERAL TRANSCRIPTION FACTOR IIB
N: TATA BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,4434
Polymers54,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
S: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
T: ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT
Q: GENERAL TRANSCRIPTION FACTOR IIB
R: TATA BOX BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,4434
Polymers54,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.450, 122.298, 140.217
Angle α, β, γ (deg.)90.00, 113.08, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

-
Components

#1: DNA chain
ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT


Mass: 5630.655 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: NATURAL SEQUENCE OF ADENOVIRAL MAJOR LATE PROMOTER
#2: DNA chain
ADMLP TATA-BOX DNA CONTAINING IIB RECOGNITION ELEMENT


Mass: 5403.492 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: NATURAL SEQUENCE OF ADENOVIRAL MAJOR LATE PROMOTER
#3: Protein
GENERAL TRANSCRIPTION FACTOR IIB / TRANSCRIPTION INITIATION FACTOR IIB / TFIIBC


Mass: 23110.922 Da / Num. of mol.: 5 / Fragment: C-TERMINAL CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403
#4: Protein
TATA BOX BINDING PROTEIN / TATA-BOX FACTOR / TATA SEQUENCE-BINDING PROTEIN / TBPC


Mass: 20298.098 Da / Num. of mol.: 5 / Fragment: C-TERMINAL CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: P20226
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
PH range: 5.6-7.5
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS.HCL11
2AMMONIUM ACETATE11
3MGCL211
4KCL11
5SODIUM CITRATE11
6DTT11
7GLYCEROL11
8PEG 800011
9GLYCEROL12
10PEG 800012
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
24 %(w/v)PEG80001reservoir
350 mMTris-HCl1reservoir
450 mM1reservoirMgCl2
5100 mMsodium citrate1reservoir
610 %glycerol1reservoir
71
81
91
101

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.013
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.013 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 101892 / Num. obs: 101892 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.98 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 2.25 % / Rmerge(I) obs: 0.341 / % possible all: 85.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 85.4 % / Mean I/σ(I) obs: 2.9

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.65→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1478756.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: USED BULK SOLVENT CORRECTION, AND MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4854 5.1 %RANDOM
Rwork0.229 ---
all0.237 99505 --
obs0.231 95770 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.95 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å27.48 Å2
2--4.49 Å20 Å2
3----2.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15210 3660 0 329 19199
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 541 5.2 %
Rwork0.346 9900 -
obs--58.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 90918
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.35

+
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