+Open data
-Basic information
Entry | Database: PDB / ID: 2gmi | ||||||
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Title | Mms2/Ubc13~Ubiquitin | ||||||
Components |
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Keywords | LIGASE / HUMAN PROTEIN / ubiquitin / Ubc13 / Mms2 / E2 / UEV / Ubc13 ubiquitin covalent complex | ||||||
Function / homology | Function and homology information protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / postreplication repair / E2 ubiquitin-conjugating enzyme / fungal-type vacuole membrane ...protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / postreplication repair / E2 ubiquitin-conjugating enzyme / fungal-type vacuole membrane / ligase activity / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wolberger, C. / Eddins, M.J. / Carlile, C.M. / Gomez, K.G. / Pickart, C.M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation. Authors: Eddins, M.J. / Carlile, C.M. / Gomez, K.M. / Pickart, C.M. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gmi.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gmi.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gmi_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 2gmi_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 2gmi_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2gmi_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/2gmi ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gmi | HTTPS FTP |
-Related 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: 17344.805 Da / Num. of mol.: 1 / Mutation: C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC13 / Production host: Escherichia coli (E. coli) / References: UniProt: P52490, ubiquitin-protein ligase |
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#2: Protein | Mass: 15565.644 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MMS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P53152 |
#3: Protein | Mass: 8576.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q867C3, UniProt: P0CG48*PLUS |
#4: 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: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 17% PEG 1000, 100 mM Na/K phosphate, pH 6.2, 25 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0039 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0039 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 14242 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rsym value: 0.054 / Net I/σ(I): 44 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.301 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JAT, 1UBQ Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 27.364 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.474 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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