+Open data
-Basic information
Entry | Database: PDB / ID: 7xys | ||||||||||||
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Title | Crystal structure of ZER1 bound to SFLH degron | ||||||||||||
Components | Protein zer-1 homolog | ||||||||||||
Keywords | LIGASE / E3 | ||||||||||||
Function / homology | Function and homology information Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Dong, C. / Yan, X. / Li, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation. Authors: Li, Y. / Zhao, Y. / Yan, X. / Ye, C. / Weirich, S. / Zhang, B. / Wang, X. / Song, L. / Jiang, C. / Jeltsch, A. / Dong, C. / Mi, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xys.cif.gz | 244.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xys.ent.gz | 191.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/7xys ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xys | HTTPS FTP |
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-Related structure data
Related structure data | 7xytC 7xyuC 7xyvC 7xywC 7xyxC 7ep3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29324.936 Da / Num. of mol.: 4 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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4F, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.07 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-h-l / Fraction: 0.42 |
Reflection | Resolution: 1.7→48.53 Å / Num. obs: 116008 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.33 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.453 / Num. unique obs: 36520 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EP3 Resolution: 1.7→36.72 Å / Cross valid method: THROUGHOUT / σ(F): 53.65 / Phase error: 30.38 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.32 Å2 / Biso mean: 17.7899 Å2 / Biso min: 5.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→36.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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