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Yorodumi- PDB-2w2h: Structural basis of transcription activation by the Cyclin T1-Tat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w2h | ||||||
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Title | Structural basis of transcription activation by the Cyclin T1-Tat-TAR RNA complex from EIAV | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / RNA-BINDING PROTEIN / TAR / TAT / CYCLIN / NUCLEUS / ACTIVATOR / CYCLIN T1 / HOST-VIRUS INTERACTION / TRANSCRIPTION REGULATION / CELL CYCLE / RNA-BINDING / ACETYLATION / COILED COIL / TRANSCRIPTION / CELL DIVISION / CRYSTALLIZATION | ||||||
Function / homology | Function and homology information 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / host cell nucleolus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / cell cycle / cyclin-dependent protein serine/threonine kinase regulator activity / RNA-binding transcription regulator activity / viral process ...7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / host cell nucleolus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / cell cycle / cyclin-dependent protein serine/threonine kinase regulator activity / RNA-binding transcription regulator activity / viral process / cell division / DNA-templated transcription / host cell nucleus / regulation of transcription by RNA polymerase II / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | EQUUS CABALLUS (horse) EQUINE INFECTIOUS ANEMIA VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Anand, K. / Geyer, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural Insights Into the Cyclin T1-Tat-Tar RNA Transcription Activation Complex from Eiav. Authors: Anand, K. / Schulte, A. / Vogel-Bachmayr, K. / Scheffzek, K. / Geyer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w2h.cif.gz | 306.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w2h.ent.gz | 248.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w2h_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
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Full document | 2w2h_full_validation.pdf.gz | 562.6 KB | Display | |
Data in XML | 2w2h_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 2w2h_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/2w2h ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w2h | HTTPS FTP |
-Related structure data
Related structure data | 2pk2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (0.0005, -1, 0.0094), Vector: |
-Components
#1: Protein | Mass: 30843.354 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-267 Source method: isolated from a genetically manipulated source Details: GENBANK\: AF137509 / Source: (gene. exp.) EQUUS CABALLUS (horse) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XT26 #2: Protein/peptide | Mass: 3493.091 Da / Num. of mol.: 2 Fragment: CYCLIN BOX DOMAIN OF EQUINE CYCLIN T1, RESIDUES 47-75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EQUINE INFECTIOUS ANEMIA VIRUS / Strain: PGEX-4T1 / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20920 #3: RNA chain | Mass: 7027.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PURIFIED SINGLE-STRANDED DNA OLIGONUCLEOTIDES / Source: (synth.) EQUINE INFECTIOUS ANEMIA VIRUS #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | CYCLIN T1- TAT IS FUSION COMPLEX. MUTATION IN NUCLEOTIDE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 7% PEG 8000, 0.1M HEPES PH7.4 0.1 M AMMONIUM SULPHATE, 15 MM MNCL2, 5% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 30, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→30 Å / Num. obs: 22461 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 103.83 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.74 |
Reflection shell | Resolution: 3.2→3.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 8.74 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PK2 Resolution: 3.25→29.927 Å / SU ML: 0.46 / σ(F): 1.41 / Phase error: 30.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 114.396 Å2 / ksol: 0.274 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 137.69 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→29.927 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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