+Open data
-Basic information
Entry | Database: PDB / ID: 8ypu | ||||||
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Title | Cryo-EM structure of ButCD complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / transporter / TonB-dependent | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
Authors | Xu, J.H. / Chen, Z. / Gao, X. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues Authors: Xu, J.H. / Chen, Z. / Gao, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ypu.cif.gz | 546.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ypu.ent.gz | 443.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ypu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ypu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ypu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ypu_validation.xml.gz | 81.6 KB | Display | |
Data in CIF | 8ypu_validation.cif.gz | 121.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/8ypu ftp://data.pdbj.org/pub/pdb/validation_reports/yp/8ypu | HTTPS FTP |
-Related structure data
Related structure data | 39494MC 8yptC 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: 48007.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides fragilis (bacteria) / References: UniProt: A0A2M9UVJ9 #2: Protein | Mass: 111314.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteroides fragilis (bacteria) / References: UniProt: A0A642HUG1 |
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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: ButCD complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Bacteroides fragilis (bacteria) |
Buffer solution | pH: 8 |
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: 500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 619121 / Symmetry type: POINT |