+Open data
-Basic information
Entry | Database: PDB / ID: 4c46 | ||||||
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Title | ANDREI-N-LVPAS fused to GCN4 adaptors | ||||||
Components | GENERAL CONTROL PROTEIN GCN4, GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | TRANSCRIPTION / ION COORDINATION / POLAR CORE RESIDUES / FUSION PROTEIN / CHIMERA / COILED COIL / PROLINE | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Albrecht, R. / Alva, V. / Ammelburg, M. / Baer, K. / Basina, E. / Boichenko, I. / Bonhoeffer, F. / Braun, V. / Chaubey, M. / Chauhan, N. ...Albrecht, R. / Alva, V. / Ammelburg, M. / Baer, K. / Basina, E. / Boichenko, I. / Bonhoeffer, F. / Braun, V. / Chaubey, M. / Chauhan, N. / Chellamuthu, V.R. / Coles, M. / Deiss, S. / Ewers, C.P. / Forouzan, D. / Fuchs, A. / Groemping, Y. / Hartmann, M.D. / Hernandez Alvarez, B. / Jeganantham, A. / Kalev, I. / Koenninger, U. / Koiwai, K. / Kopec, K.O. / Korycinski, M. / Laudenbach, B. / Lehmann, K. / Leo, J.C. / Linke, D. / Marialke, J. / Martin, J. / Mechelke, M. / Michalik, M. / Noll, A. / Patzer, S.I. / Scharfenberg, F. / Schueckel, M. / Shahid, S.A. / Sulz, E. / Ursinus, A. / Wuertenberger, S. / Zhu, H. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2014 Title: Your Personalized Protein Structure: Andrei N. Lupas Fused to GCN4 Adaptors. Authors: Deiss, S. / Hernandez Alvarez, B. / Bar, K. / Ewers, C.P. / Coles, M. / Albrecht, R. / Hartmann, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c46.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c46.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c46 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c46 | HTTPS FTP |
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-Related structure data
Related structure data | 1gcmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8869.462 Da / Num. of mol.: 3 / Fragment: RESIDUES 250-278,250-278 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ANDREI-N-LVPAS FUSED TO GCN4 ADAPTORS Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069 #2: Chemical | ChemComp-BR / | #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4 Details: SITTING DROP, PROTEIN SOLUTION 50 MM NACL AND 50 MM SODIUM ACETATE PH 4.0, RESERVOUR SOLUTION 0.1 M HEPES PH 7.5 1.75 M SODIUM BROMIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→36.6 Å / Num. obs: 16104 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.94 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCM Resolution: 1.95→36.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.125 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.801 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→36.64 Å
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