+Open data
-Basic information
Entry | Database: PDB / ID: 8p2e | ||||||||||||
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Title | Homotypic interacting B1 fab bound to Chondroitin Sulfate A | ||||||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / Chondroitin Sulfate A | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Raghavan, S.S.R. / Dagil, R. / Wang, K.T. / Salanti, A. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: To Be Published Title: Structure of homotypic B1 fabs bound to Chondroiting Sulfate A Authors: Raghavan, S.S.R. / Vidal-Calvo, E.E. / Dagil, R. / Wang, K.T. / Salanti, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p2e.cif.gz | 318.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p2e.ent.gz | 260.1 KB | Display | PDB format |
PDBx/mmJSON format | 8p2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p2e_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8p2e_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8p2e_validation.xml.gz | 56.9 KB | Display | |
Data in CIF | 8p2e_validation.cif.gz | 84.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/8p2e ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p2e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 23662.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 26419.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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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: B1 fabs bound to chondroitin sulphate A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 50 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) |
Buffer solution | pH: 7.5 |
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: 2800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1250000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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