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- PDB-1f3u: CRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF -

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Basic information

Entry
Database: PDB / ID: 1f3u
TitleCRYSTAL STRUCTURE OF THE RAP30/74 INTERACTION DOMAINS OF HUMAN TFIIF
Components
  • TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT
  • TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
KeywordsTRANSCRIPTION / general transcription initiation and elongation factor / RNA polymerase II / novel dimerization fold / beta barrel
Function / homology
Function and homology information


phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA polymerase II general transcription initiation factor binding / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE ...phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA polymerase II general transcription initiation factor binding / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / 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 / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / negative regulation of protein binding / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / response to virus / microtubule cytoskeleton / cell junction / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / protein domain specific binding / intracellular membrane-bounded organelle / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
General transcription factor IIF subunit 2 / General transcription factor IIF subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsGaiser, F. / Tan, S. / Richmond, T.J.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution.
Authors: Gaiser, F. / Tan, S. / Richmond, T.J.
#1: Journal: Protein Expr.Purif. / Year: 1994
Title: Importance of Codon Preference for Production of Human RAP74 and Reconstitution of the RAP30/74 Complex
Authors: Wang, B.Q. / Lei, L. / Burton, Z.F.
History
DepositionJun 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
B: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT
C: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
D: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT
E: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
F: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT
G: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
H: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)130,6438
Polymers130,6438
Non-polymers00
Water12,466692
1
A: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
B: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)32,6612
Polymers32,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-25 kcal/mol
Surface area16600 Å2
MethodPISA
2
C: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
D: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)32,6612
Polymers32,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-23 kcal/mol
Surface area17440 Å2
MethodPISA
3
E: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
F: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)32,6612
Polymers32,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-22 kcal/mol
Surface area17600 Å2
MethodPISA
4
G: TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT
H: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)32,6612
Polymers32,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-25 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.015, 72.290, 82.266
Angle α, β, γ (deg.)104.51, 93.32, 104.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TRANSCRIPTION INITIATION FACTOR IIF, BETA SUBUNIT / TRANSCRIPTION INITIATION FACTOR RAP30


Mass: 12718.334 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P13984
#2: Protein
TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT / TRANSCRIPTION INITIATION FACTOR RAP74


Mass: 19942.447 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P35269
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1500, lithium nitrate, bis-Tris, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 7 / PH range high: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
213-15 %PEG15001drop
375 mM1dropLiNO3
432.5 mMBis-Tris1drop
51 mMdithiothreitol1drop
618-20 %PEG15001reservoir
7100 mM1reservoirLiNO3
850 mMBis-Tris1reservoir
91 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→67 Å / Num. obs: 108916 / % possible obs: 96.8 % / Redundancy: 2.2 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.194 / Num. unique all: 10429 / % possible all: 92.9

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementResolution: 1.7→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1277208.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The values were calculated with all atoms at zero occupancy deleted. Refmac was also used for part of the refinement process. Alternate position indicators represent two completely different ...Details: The values were calculated with all atoms at zero occupancy deleted. Refmac was also used for part of the refinement process. Alternate position indicators represent two completely different chain traces that are induced by a crystal contact. If the corresponding conformation B is missing, this indicates that this branch of the chain is not observed.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3596 3.4 %RANDOM
Rwork0.225 ---
obs-105675 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 113.4 Å2 / ksol: 0.68 e/Å3
Displacement parametersBiso mean: 45.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å22.79 Å23.74 Å2
2---1.64 Å2-1.22 Å2
3---2.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8236 0 0 692 8928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d26.23
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it4.273
X-RAY DIFFRACTIONc_mcangle_it5.774
X-RAY DIFFRACTIONc_scbond_it6.575
X-RAY DIFFRACTIONc_scangle_it8.426
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.323 388 4.1 %
Rwork0.293 9154 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9A / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3.4 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it3
X-RAY DIFFRACTIONc_scbond_it5
X-RAY DIFFRACTIONc_mcangle_it4
X-RAY DIFFRACTIONc_scangle_it6
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / % reflection Rfree: 4.1 % / Rfactor Rwork: 0.293 / Rfactor obs: 0.293

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