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Yorodumi- PDB-7v6o: MERS S ectodomain trimer in complex with neutralizing antibody 11... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v6o | ||||||
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Title | MERS S ectodomain trimer in complex with neutralizing antibody 111 (state 2) | ||||||
Components |
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Keywords | PROTEIN BINDING / MERS / spike / antibody | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human betacoronavirus 2c EMC/2012 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.56 Å | ||||||
Authors | Wang, X. / Zhao, J. / Wang, Z. / Zeng, J. / Zhang, S. / Wang, Y. | ||||||
Funding support | 1items
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Citation | Journal: to be published Title: MERS S ectodomain trimer in complex with neutralizing antibody 111 (state 2) Authors: Wang, X. / Zhao, J. / Wang, Z. / Zeng, J. / Zhang, S. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v6o.cif.gz | 780.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v6o.ent.gz | 633.5 KB | Display | PDB format |
PDBx/mmJSON format | 7v6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v6o_validation.pdf.gz | 738.9 KB | Display | wwPDB validaton report |
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Full document | 7v6o_full_validation.pdf.gz | 800 KB | Display | |
Data in XML | 7v6o_validation.xml.gz | 112.3 KB | Display | |
Data in CIF | 7v6o_validation.cif.gz | 175.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/7v6o ftp://data.pdbj.org/pub/pdb/validation_reports/v6/7v6o | HTTPS FTP |
-Related structure data
Related structure data | 31744MC 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
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 130718.586 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K0BRG7 #2: Antibody | Mass: 23786.467 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 24524.377 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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: MERS spike glycoprotein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Middle East respiratory syndrome-related coronavirus |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 4.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1463548 / Symmetry type: POINT |