+Open data
-Basic information
Entry | Database: PDB / ID: 7nh3 | ||||||
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Title | Nematocida Huwe1 in open conformation. | ||||||
Components | E3 ubiquitin-protein ligase HUWE1 | ||||||
Keywords | LIGASE / Huwe1 / Nematocida / E3 Ligase / HECT | ||||||
Function / homology | Function and homology information HECT-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / membrane Similarity search - Function | ||||||
Biological species | Nematocida sp. ERTm5 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.37 Å | ||||||
Authors | Petrova, O. / Grishkovskaya, I. / Grabarczyk, D.B. / Kessler, D. / Haselbach, D. / Clausen, T. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of HUWE1: One ring to ubiquitinate them all Authors: Grabarrczyk, D.B. / Petrova, O.A. / Haselbach, D. / Kessler, D. / Clausen, T. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nh3.cif.gz | 535.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nh3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nh3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7nh3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7nh3_validation.xml.gz | 76.5 KB | Display | |
Data in CIF | 7nh3_validation.cif.gz | 111.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nh3 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nh3 | HTTPS FTP |
-Related structure data
Related structure data | 12319MC 12318 7nh1 M: map data used to model this data 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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-Components
#1: Protein | Mass: 287751.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nematocida sp. ERTm5 (fungus) / Gene: NEIG_01557 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A177ELV2 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Huwe1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.287 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Nematocida sp. ERTm5 (fungus) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 4 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 |
-Processing
Software | Name: PHENIX / Version: 1.19_4080: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57866 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7BII Accession code: 7BII / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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