+Open data
-Basic information
Entry | Database: PDB / ID: 8kfa | |||||||||
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Title | Cryo-EM structure of HSV-1 gB with D48 Fab complex | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HSV-1 gB / fab / neutralizing antibody / complex / Cryo-EM / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human herpesvirus 1 (Herpes simplex virus type 1) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Yang, J. / Sun, C. / Fang, X. / Zeng, M. / Liu, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: hlife / Year: 2023 Title: The structure of HSV-1 gB bound to a potent neutralizing antibody reveals a conservative antigenic domain across herpesviruses Authors: Sun, C. / Yang, J.W. / Xie, C. / Fang, X.Y. / Bu, G.L. / Zhao, G.X. / Dai, D.L. / Liu, Z. / Zeng, M.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kfa.cif.gz | 433.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kfa.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8kfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kfa_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8kfa_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8kfa_validation.xml.gz | 82.4 KB | Display | |
Data in CIF | 8kfa_validation.cif.gz | 122.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/8kfa ftp://data.pdbj.org/pub/pdb/validation_reports/kf/8kfa | HTTPS FTP |
-Related structure data
Related structure data | 37203MC 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: Antibody | Mass: 24742.861 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23476.164 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: Protein | Mass: 70337.844 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (strain KOS) / Gene: gB, UL27 / Production host: Homo sapiens (human) / References: UniProt: P06437 |
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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: Cryo-EM structure of HSV-1 gB with D48 Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Specimen | 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: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 1.56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168888 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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