+Open data
-Basic information
Entry | Database: PDB / ID: 8pba | |||||||||||||||
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Title | Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo) | |||||||||||||||
Components | Dipeptidyl Peptidase Four (IV) family | |||||||||||||||
Keywords | HYDROLASE / Dipeptidylpeptidase | |||||||||||||||
Function / homology | Function and homology information dipeptidyl-peptidase activity / serine-type peptidase activity / proteolysis Similarity search - Function | |||||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||||||||
Authors | Gudipati, R.K. / Cavadini, S. / Kempf, G. / Grosshans, H. | |||||||||||||||
Funding support | Switzerland, Poland, 4items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo) Authors: Gudipati, R.K. / Cavadini, S. / Kempf, G. / Grosshans, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pba.cif.gz | 540.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pba.ent.gz | 446.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pba_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8pba_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8pba_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 8pba_validation.cif.gz | 76.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pba ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pba | HTTPS FTP |
-Related structure data
Related structure data | 17582MC 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: 106462.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dpf-3, CELE_K02F2.1, K02F2.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q965K3 |
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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: Homodimeric complex of DPF-3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
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: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223429 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |