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- PDB-1c9b: CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOM... -

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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 / meiotic sister chromatid cohesion / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / 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 / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter ...positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / RNA polymerase transcription factor SL1 complex / RNA polymerase III general transcription initiation factor activity / 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 / transcriptional start site selection at RNA polymerase II 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 / germinal vesicle / RNA Polymerase I Transcription Termination / transcription preinitiation complex / nuclear thyroid hormone receptor binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / cell division site / protein acetylation / 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 / acetyltransferase activity / RNA polymerase II complex binding / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / viral transcription / TFIIB-class transcription factor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / DNA-templated transcription initiation / protein-DNA complex / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / euchromatin / B-WICH complex positively regulates rRNA expression / kinetochore / RNA polymerase II transcription regulator complex / chromosome / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / 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 / cytoplasm
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. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / 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. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 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

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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

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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

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