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Yorodumi- PDB-7nvk: Crystal structure of UBA5 fragment fused to the N-terminus of UFC1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nvk | ||||||
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Title | Crystal structure of UBA5 fragment fused to the N-terminus of UFC1 | ||||||
Components | Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1 | ||||||
Keywords | LIGASE / Ubiquitin like fold modifier enzyme 5 (UBA5) / E1 / Ubiquitin fold modifier 1 (UFM1) / Ubiquitin fold modifier conjugating enzyme 1 (UFC1) / UFMYLATION | ||||||
Function / homology | Function and homology information UFM1 conjugating enzyme activity / UFM1 activating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization ...UFM1 conjugating enzyme activity / UFM1 activating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization / response to endoplasmic reticulum stress / erythrocyte differentiation / brain development / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / zinc ion binding / extracellular exosome / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å | ||||||
Authors | Manoj Kumar, P. / Padala, P. / Isupov, M.N. / Wiener, R. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for UFM1 transfer from UBA5 to UFC1. Authors: Kumar, M. / Padala, P. / Fahoum, J. / Hassouna, F. / Tsaban, T. / Zoltsman, G. / Banerjee, S. / Cohen-Kfir, E. / Dessau, M. / Rosenzweig, R. / Isupov, M.N. / Schueler-Furman, O. / Wiener, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nvk.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nvk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nvk_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 7nvk_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 7nvk_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7nvk_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvk ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvk | HTTPS FTP |
-Related structure data
Related structure data | 7nvjC 7nw1C 2z6oS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25917.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1, UFC1, CGI-126, HSPC155 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9, UniProt: Q9Y3C8 |
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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: 2.51 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% (v/v) Tacsimate pH 7.0, 20% PEG 3350, 0.1M HEPES pH 7.5, 6mM zinc sulfate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→46.78 Å / Num. obs: 7314 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 127.1 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.112 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 21.4 % / Num. unique obs: 953 / CC1/2: 0.292 / Rrim(I) all: 0.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6O Resolution: 2.651→46.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.968 / SU B: 23.987 / SU ML: 0.466 / Cross valid method: NONE / ESU R: 0.723 / ESU R Free: 0.33 Details: Hydrogens have been added in their 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 / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 157.069 Å2
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Refinement step | Cycle: LAST / Resolution: 2.651→46.78 Å
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Refine LS restraints |
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LS refinement shell |
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