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Yorodumi- PDB-6h9m: Coiled-coil domain-containing protein 90B residues 43-125 from Ho... -
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-Basic information
Entry | Database: PDB / ID: 6h9m | ||||||
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Title | Coiled-coil domain-containing protein 90B residues 43-125 from Homo sapiens fused to a GCN4 adaptor | ||||||
Components | Coiled-coil domain-containing protein 90B, mitochondrial,General control protein GCN4 | ||||||
Keywords | MEMBRANE PROTEIN / coiled coil / beta-layer / mitochondrial membrane | ||||||
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 RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / amino acid biosynthetic process / cellular response to nutrient levels / cellular response to amino acid starvation / mitochondrial membrane / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / membrane => GO:0016020 / 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 / mitochondrion / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Adlakha, J. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. / Hartmann, M.D. | ||||||
Citation | Journal: Structure / Year: 2019 Title: Characterization of MCU-Binding Proteins MCUR1 and CCDC90B - Representatives of a Protein Family Conserved in Prokaryotes and Eukaryotic Organelles. Authors: Adlakha, J. / Karamichali, I. / Sangwallek, J. / Deiss, S. / Bar, K. / Coles, M. / Hartmann, M.D. / 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 | 6h9m.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h9m.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 6h9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h9m_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 6h9m_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 6h9m_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6h9m_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9m ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9m | HTTPS FTP |
-Related structure data
Related structure data | 6h9lC 5apqS S: Starting model for refinement C: citing same article (ref.) |
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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: Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 62 - 155 / Label seq-ID: 23 - 116
NCS ensembles :
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-Components
#1: Protein | Mass: 13569.512 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: CCDC90B, CUA003, MDS011, MDS025, GCN4, AAS3, ARG9, YEL009C Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZT6, 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: 1.93 Å3/Da / Density % sol: 36.33 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: Molecular Dimensions Morpheus Screen, Well F2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0703 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0703 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.3 Å / Num. obs: 19522 / % possible obs: 99.8 % / Redundancy: 6.27 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 6.46 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.89 / CC1/2: 0.835 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5APQ Resolution: 2.1→37.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU B: 15.664 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.699 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→37.27 Å
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Refine LS restraints |
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