+Open data
-Basic information
Entry | Database: PDB / ID: 7v4t | ||||||||||||||||||
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Title | Cryo-EM structure of Alphavirus M1 | ||||||||||||||||||
Components |
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Keywords | VIRUS / Alphavirus M1 | ||||||||||||||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane ...T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Alphavirus M1 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.04 Å | ||||||||||||||||||
Authors | Gao, Y. / Jia, X. / Zhang, Q. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: To Be Published Title: Cryo-EM evidence of viral N-glycosylation reveal receptor binding mechanisms of alphavirus M1 Authors: Song, D. / Jia, X. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v4t.cif.gz | 694.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v4t.ent.gz | 576.8 KB | Display | PDB format |
PDBx/mmJSON format | 7v4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v4t_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7v4t_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7v4t_validation.xml.gz | 122.9 KB | Display | |
Data in CIF | 7v4t_validation.cif.gz | 184.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/7v4t ftp://data.pdbj.org/pub/pdb/validation_reports/v4/7v4t | HTTPS FTP |
-Related structure data
Related structure data | 31716MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 47595.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alphavirus M1 / References: UniProt: A0MNM2 #2: Protein | Mass: 46462.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alphavirus M1 / References: UniProt: A0MNM2 #3: Protein | Mass: 30084.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alphavirus M1 / References: UniProt: A0MNM2 #4: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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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: Alphavirus M1 / Type: VIRUS / Entity ID: #1-#3 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Alphavirus M1 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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 |
Image recording | Electron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32894 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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