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- PDB-8pba: Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo) -

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Basic information

Entry
Database: PDB / ID: 8pba
TitleCryo-EM structure of Caenorhabditis elegans DPF-3 (apo)
ComponentsDipeptidyl Peptidase Four (IV) family
KeywordsHYDROLASE / Dipeptidylpeptidase
Function / homologyDipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / dipeptidyl-peptidase activity / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / serine-type peptidase activity / Alpha/Beta hydrolase fold / proteolysis / Dipeptidyl Peptidase Four (IV) family
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsGudipati, R.K. / Cavadini, S. / Kempf, G. / Grosshans, H.
Funding support Switzerland, Poland, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation182880 Switzerland
Other private
Polish National Science CentreSONATA BIS 2021/42/E/NZ1/00336 Poland
Polish National Science CentreOPUS 2022/45/B/NZ2/02183 Poland
CitationJournal: To Be Published
Title: Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo)
Authors: Gudipati, R.K. / Cavadini, S. / Kempf, G. / Grosshans, H.
History
DepositionJun 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl Peptidase Four (IV) family
B: Dipeptidyl Peptidase Four (IV) family


Theoretical massNumber of molelcules
Total (without water)212,9262
Polymers212,9262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Dipeptidyl Peptidase Four (IV) family


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homodimeric complex of DPF-3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
4GctfCTF correction
5cryoSPARCCTF correction
6RELIONCTF correction
9Cootmodel fitting
10ISOLDEmodel fitting
12RosettaEMmodel refinement
13cryoSPARCinitial Euler assignment
15RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223429 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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