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Yorodumi- PDB-2k07: Solution NMR structure of human E2-like ubiquitin-fold modifier c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k07 | |||||||||
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Title | Solution NMR structure of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). Northeast Structural Genomics Consortium target HR41 | |||||||||
Components | Ufm1-conjugating enzyme 1 | |||||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ufc1 / Ubiquitin Conjugating Enzyme / E2 / Ufm1 / Polymorphism / Ubl conjugation pathway / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | |||||||||
Function / homology | Function and homology information UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / molecular dynamics, simulated annealing, distance geometry, torsion angle dynamics | |||||||||
Authors | Liu, G. / Eletsky, A. / Atreya, H.S. / Aramini, J.M. / Xiao, R. / Acton, T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2009 Title: NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. Authors: Liu, G. / Forouhar, F. / Eletsky, A. / Atreya, H.S. / Aramini, J.M. / Xiao, R. / Huang, Y.J. / Abashidze, M. / Seetharaman, J. / Liu, J. / Rost, B. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Szyperski, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k07.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2k07.ent.gz | 942.3 KB | Display | PDB format |
PDBx/mmJSON format | 2k07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k07_validation.pdf.gz | 341.8 KB | Display | wwPDB validaton report |
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Full document | 2k07_full_validation.pdf.gz | 471.2 KB | Display | |
Data in XML | 2k07_validation.xml.gz | 66 KB | Display | |
Data in CIF | 2k07_validation.cif.gz | 87.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/2k07 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/2k07 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20557.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y3C8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.1 mM [U-100% 13C; U-100% 15N] protein UFC1, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 1.1 mM / Component: Protein UFC1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: na / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics, simulated annealing, distance geometry, torsion angle dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |