+Open data
-Basic information
Entry | Database: PDB / ID: 7ep5 | ||||||||||||
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Title | Crystal structure of ZER1 bound to GKLH degron | ||||||||||||
Components | Protein zer-1 homolog | ||||||||||||
Keywords | LIGASE / E3 ligase | ||||||||||||
Function / homology | Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich repeat domain superfamily / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Armadillo-like helical / Armadillo-type fold / Protein zer-1 homolog Function and homology information | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||||||||
Authors | Yan, X. / Li, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Mol.Cell / Year: 2021 Title: Molecular basis for recognition of Gly/N-degrons by CRL2 ZYG11B and CRL2 ZER1 . Authors: Yan, X. / Li, Y. / Wang, G. / Zhou, Z. / Song, G. / Feng, Q. / Zhao, Y. / Mi, W. / Ma, Z. / Dong, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ep5.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ep5.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ep5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7ep5 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7ep5 | HTTPS FTP |
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-Related structure data
Related structure data | 7ep0SC 7ep1C 7ep2C 7ep3C 7ep4C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29276.916 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZER1, C9orf60, ZYG, ZYG11BL / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z7L7 #2: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.22 M Ammonium formate and 18% (wt/vol) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979191 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→52.8 Å / Num. obs: 39427 / % possible obs: 99.4 % / Redundancy: 11.3 % / Biso Wilson estimate: 30.67 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.02→2.07 Å / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2746 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EP0 Resolution: 2.02→52.8 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 32.68 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→52.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.092 Å
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