+Open data
-Basic information
Entry | Database: PDB / ID: 7nw1 | ||||||
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Title | Crystal structure of UFC1 in complex with UBA5 | ||||||
Components |
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Keywords | LIGASE / Ubiquitin like fold modifier enzyme 5 (UBA5) / E1 / Ubiquitin fold modifier 1 (UFM1) / Ubiquitin fold modifier conjugating enzyme2 (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: 1.95 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 | 7nw1.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nw1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nw1_validation.pdf.gz | 495.1 KB | Display | wwPDB validaton report |
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Full document | 7nw1_full_validation.pdf.gz | 508.2 KB | Display | |
Data in XML | 7nw1_validation.xml.gz | 17 KB | Display | |
Data in CIF | 7nw1_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/7nw1 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/7nw1 | HTTPS FTP |
-Related structure data
Related structure data | 7nvjC 7nvkC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules AAABBBCCCFFF
#1: Protein | Mass: 19543.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8 #2: Protein/peptide | Mass: 1801.069 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9 |
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-Non-polymers , 5 types, 70 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.13 Å3/Da / Density % sol: 42.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→33.71 Å / Num. obs: 15162 / % possible obs: 46.5 % / Redundancy: 8.3 % / Biso Wilson estimate: 49.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.132 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 6.8 % / Num. unique obs: 152 / CC1/2: 0.478 / Rrim(I) all: 1.87 / % possible all: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z6O Resolution: 1.95→23.761 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: NONE / ESU R: 0.662 / 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: 59.743 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→23.761 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: 20
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