+Open data
-Basic information
Entry | Database: PDB / ID: 4lad | ||||||
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Title | Crystal Structure of the Ube2g2:RING-G2BR complex | ||||||
Components |
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Keywords | LIGASE/LIGASE / E2:E3 complex / LIGASE-LIGASE complex | ||||||
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 / BAT3 complex binding / Derlin-1 retrotranslocation complex / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / ubiquitin conjugating enzyme activity ...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 / BAT3 complex binding / Derlin-1 retrotranslocation complex / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / ubiquitin conjugating enzyme activity / non-canonical NF-kappaB signal transduction / protein K48-linked ubiquitination / cellular response to interferon-beta / protein autoubiquitination / 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 / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / ubiquitin-dependent protein catabolic process / positive regulation of protein binding / growth cone / protein-folding chaperone binding / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / protein-containing complex / ATP binding / membrane / metal ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Liang, Y.-H. / Li, J. / Das, R. / Byrd, R.A. / Ji, X. | ||||||
Citation | Journal: Embo J. / Year: 2013 Title: Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. Authors: Das, R. / Liang, Y.H. / Mariano, J. / Li, J. / Huang, T. / King, A. / Tarasov, S.G. / Weissman, A.M. / Ji, X. / Byrd, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lad.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lad.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4lad ftp://data.pdbj.org/pub/pdb/validation_reports/la/4lad | HTTPS FTP |
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-Related structure data
Related structure data | 2lxhC 2lxpC 3h8kS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18582.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2, Ubiquitin-conjugating enzyme E2G2 isoform 1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(star) / References: UniProt: P60604, ubiquitin-protein ligase | ||||
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#2: Protein | Mass: 15471.062 Da / Num. of mol.: 1 Fragment: RING region (UNP residues 313-393) and G2BR region (UNP residues 574-600) Mutation: 40 a.a. insertion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, Autocrine motility factor receptor, RNF45 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(star) References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||
#3: Chemical | #4: Chemical | #5: 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: 1.97 Å3/Da / Density % sol: 37.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG-3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→40 Å / Num. all: 12528 / Num. obs: 12528 / % possible obs: 96.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.044 / Χ2: 1.071 / Net I/σ(I): 18.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H8K Resolution: 2.3→39.123 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.7449 / SU ML: 0.41 / σ(F): 1.35 / Phase error: 30.29 / 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: 49.368 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.62 Å2 / Biso mean: 61.0837 Å2 / Biso min: 35.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.123 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: 7
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