[English] 日本語
Yorodumi- PDB-2wg5: Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wg5 | ||||||
---|---|---|---|---|---|---|---|
Title | Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from Archaeoglobus fulgidus fused to GCN4 | ||||||
Components | GENERAL CONTROL PROTEIN GCN4, PROTEASOME-ACTIVATING NUCLEOTIDASE | ||||||
Keywords | TRANSCRIPTION / HYDROLASE / TRANSCRIPTION HYDROLASE COMPLEX / NUCLEOTIDE-BINDING / SUBSTRATE RECOGNITION / COILED COIL / AAA PROTEIN / CHAPERONE ACTIVITY / ATPASE / OB FOLD / CYTOPLASM / PROTEASOME / ATP-BINDING AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / NUCLEUS / DNA-BINDING / ACTIVATOR / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information proteasome-activating nucleotidase complex / 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 / cytosolic proteasome complex / nitrogen catabolite activation of transcription from RNA polymerase II promoter ...proteasome-activating nucleotidase complex / 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 / cytosolic proteasome complex / nitrogen catabolite activation of transcription from RNA polymerase II promoter / proteasome-activating activity / Oxidative Stress Induced Senescence / proteasome regulatory particle, base subcomplex / TFIID-class transcription factor complex binding / protein unfolding / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hartmann, M.D. / Djuranovic, S. / Ursinus, A. / Zeth, K. / Lupas, A.N. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Structure and Activity of the N-Terminal Substrate Recognition Domains in Proteasomal Atpases. Authors: Djuranovic, S. / Hartmann, M.D. / Habeck, M. / Ursinus, A. / Zwickl, P. / Martin, J. / Lupas, A.N. / Zeth, K. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wg5.cif.gz | 218 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wg5.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wg5_validation.pdf.gz | 507.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wg5_full_validation.pdf.gz | 515.4 KB | Display | |
Data in XML | 2wg5_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 2wg5_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wg5 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wg5 | HTTPS FTP |
-Related structure data
Related structure data | 2wfwSC 2wg6C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 12410.123 Da / Num. of mol.: 12 Fragment: N-DOMAIN (57-134) FUSED TO GCN4, RESIDUES 33-56,57-134 Source method: isolated from a genetically manipulated source Details: NATIVE COILED COIL SUBSTITUTED BY GCN4 Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: O28303, EC: 3.6.4.8 #2: Water | ChemComp-HOH / | Sequence details | FUSION PROTEIN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE |
---|---|
Crystal grow | Details: 100 MM TRIS PH 9.0, 1 M NH4H2PO4, 25% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.071 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.071 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.36 Å / Num. obs: 97626 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.28 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.95 |
Reflection shell | Resolution: 2.1→2.22 Å / Redundancy: 4.23 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.26 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WFW Resolution: 2.1→34.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.365 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→34.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|