+Open data
-Basic information
Entry | Database: PDB / ID: 5apt | ||||||
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Title | Sequence IENKADKAD inserted between GCN4 adaptors - Structure A9 | ||||||
Components | GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | STRUCTURAL PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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: 1.8 Å | ||||||
Authors | Hartmann, M.D. / Mendler, C.T. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
Citation | Journal: Elife / Year: 2016 Title: alpha / beta coiled coils. Authors: Hartmann, M.D. / Mendler, C.T. / Bassler, J. / Karamichali, I. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5apt.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5apt.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 5apt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5apt_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 5apt_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 5apt_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 5apt_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/5apt ftp://data.pdbj.org/pub/pdb/validation_reports/ap/5apt | HTTPS FTP |
-Related structure data
Related structure data | 5appC 5apqC 5apsC 5apuC 5apvC 5apwC 5apxC 5apyC 5apzC 2wpqS C: citing same article (ref.) 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:
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-Components
#1: Protein | Mass: 11394.077 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069 #2: 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Details: 1.6 M TRI-SODIUM CITRATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.7 Å / Num. obs: 24951 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.07 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WPQ Resolution: 1.8→32.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.767 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.134 / 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: 46.867 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32.58 Å
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Refine LS restraints |
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