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Yorodumi- PDB-3h8k: Crystal structure of Ube2g2 complxed with the G2BR domain of gp78... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h8k | ||||||
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Title | Crystal structure of Ube2g2 complxed with the G2BR domain of gp78 at 1.8-A resolution | ||||||
Components |
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Keywords | LIGASE / alpha beta / all alpha / Ubl conjugation pathway / Endoplasmic reticulum / Membrane / Metal-binding / Phosphoprotein / Receptor / Transmembrane / Zinc-finger | ||||||
Function / homology | Function and homology information negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / non-canonical NF-kappaB signal transduction / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding ...negative regulation of retrograde protein transport, ER to cytosol / regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / non-canonical NF-kappaB signal transduction / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / ubiquitin conjugating enzyme activity / cellular response to interferon-beta / protein K48-linked ubiquitination / protein autoubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / lipid droplet / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / protein-macromolecule adaptor activity / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Kalathur, R.C. / Das, R. / Li, J. / Byrd, R.A. / Ji, X. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. Authors: Das, R. / Mariano, J. / Tsai, Y.C. / Kalathur, R.C. / Kostova, Z. / Li, J. / Tarasov, S.G. / McFeeters, R.L. / Altieri, A.S. / Ji, X. / Byrd, R.A. / Weissman, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h8k.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h8k.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 3h8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h8k_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 3h8k_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 3h8k_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 3h8k_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/3h8k ftp://data.pdbj.org/pub/pdb/validation_reports/h8/3h8k | HTTPS FTP |
-Related structure data
Related structure data | 2cyxS 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: 18451.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P60604, ubiquitin-protein ligase |
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#2: Protein/peptide | Mass: 3552.120 Da / Num. of mol.: 1 / Fragment: Residues 573-600 / Mutation: K573W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR300 / Detector: CCD / Date: Jul 21, 2008 / Details: mirrors |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 16657 / % possible obs: 95.4 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.051 / Net I/σ(I): 22.381 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.74 / Num. unique all: 1272 / Χ2: 0.959 / % possible all: 74.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 48.91 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CYX Resolution: 1.8→43.048 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.809 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: 15822 / σ(F): 0.12 / 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: 46.284 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.34 Å2 / Biso mean: 34.205 Å2 / Biso min: 10.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→43.048 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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