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- EMDB-17582: Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo) -

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Basic information

Entry
Database: EMDB / ID: EMD-17582
TitleCryo-EM structure of Caenorhabditis elegans DPF-3 (apo)
Map dataFull map processed with LocScale.
Sample
  • Complex: Homodimeric complex of DPF-3
    • Protein or peptide: Dipeptidyl Peptidase Four (IV) family
KeywordsDipeptidylpeptidase / HYDROLASE
Function / homology: / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsGudipati RK / Cavadini S / Kempf G / Grosshans H
Funding support Switzerland, Poland, 4 items
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: Mol Syst Biol / Year: 2024
Title: Deep quantification of substrate turnover defines protease subsite cooperativity.
Authors: Rajani Kanth Gudipati / Dimos Gaidatzis / Jan Seebacher / Sandra Muehlhaeusser / Georg Kempf / Simone Cavadini / Daniel Hess / Charlotte Soneson / Helge Großhans /
Abstract: Substrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to ...Substrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to a small number of events. Here, we develop qPISA (quantitative Protease specificity Inference from Substrate Analysis) to study Dipeptidyl Peptidase Four (DPP4), a key regulator of blood glucose levels. We use mass spectrometry to quantify >40,000 peptides from a complex, commercially available peptide mixture. By analyzing changes in substrate levels quantitatively instead of focusing on qualitative product identification through a binary classifier, we can reveal cooperative interactions within DPP4's active pocket and derive a sequence motif that predicts activity quantitatively. qPISA distinguishes DPP4 from the related C. elegans DPF-3 (a DPP8/9-orthologue), and we relate the differences to the structural features of the two enzymes. We demonstrate that qPISA can direct protein engineering efforts like the stabilization of GLP-1, a key DPP4 substrate used in the treatment of diabetes and obesity. Thus, qPISA offers a versatile approach for profiling protease and especially exopeptidase specificity, facilitating insight into enzyme mechanisms and biotechnological and clinical applications.
History
DepositionJun 8, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17582.png

Downloads & links

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Map

FileDownload / File: emd_17582.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map processed with LocScale.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 236.6 Å		0.85 Å/pix.
x 280 pix.
= 236.6 Å		0.85 Å/pix.
x 280 pix.
= 236.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.37004226 - 0.92665076
Average (Standard dev.)0.0021843903 (±0.025403026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 236.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map.

Fileemd_17582_additional_1.map
AnnotationFull map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_17582_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_17582_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimeric complex of DPF-3

EntireName: Homodimeric complex of DPF-3
Components
  • Complex: Homodimeric complex of DPF-3
    • Protein or peptide: Dipeptidyl Peptidase Four (IV) family

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Supramolecule #1: Homodimeric complex of DPF-3

SupramoleculeName: Homodimeric complex of DPF-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Dipeptidyl Peptidase Four (IV) family

MacromoleculeName: Dipeptidyl Peptidase Four (IV) family / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 106.462812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MMFNFYQFLY NLQNVSPFID FSVLKQLTHT KMRENEPARF ETRSFSQLID HARSWKTEVR GMTTQGFTKI SLMRAEKDRL NMYAISSVP GTNTQSIFSV TIPLELVEKA QVADRKFELK LKSGYNVDSY IRKTPPSAEF TLQCERQRSQ VVTGISDYEI R NGKMILMA ...String:
MMFNFYQFLY NLQNVSPFID FSVLKQLTHT KMRENEPARF ETRSFSQLID HARSWKTEVR GMTTQGFTKI SLMRAEKDRL NMYAISSVP GTNTQSIFSV TIPLELVEKA QVADRKFELK LKSGYNVDSY IRKTPPSAEF TLQCERQRSQ VVTGISDYEI R NGKMILMA GDQLFRYNPL NEALAAIPIA VPDDQSSTEP MDISEGSITS GTKGSGSEAP QSSTVPPVTR IPIKKPTTST EK PATAPPT NNFVSSAKVC PADSSLLAYV LNKQVYIEKN GKIIHRTSSN SKHITNGVPS YIVQEELERF EGIWWSESKT RLL YEHVNE EKVAESQFGV NGDPPVAPMK YPRAGTKNAY STLRMVILEN GKAYDVPLKD EVIYKHCPFY EYITRAGFFS DGTT VWVQV MSRDQAQCSL LLIPYTDFLL PEELGGSIKE DNLQLSTDLN MGVWDDKSHE ETMEKPPRGK LRGTVQIHKA RNDYW INTH NAIYPLKITD EEHPMYEFIY CLEKPNGSCL ALISAELDQN GYCRHTEEKL LMAENFSINK SMGIVVDEVR ELVYYV ANE SHPTEWNICV SHYRTGQHAQ LTESGICFKS ERANGKLALD LDHGFACYMT SVGSPAECRF YSFRWKENEV LPSTVYA AN ITVSGHPGQP DLHFDSPEMI EFQSKKTGLM HYAMILRPSN FDPYKKYPVF HYVYGGPGIQ IVHNDFSWIQ YIRFCRLG Y VVVFIDNRGS AHRGIEFERH IHKKMGTVEV EDQVEGLQML AERTGGFMDM SRVVVHGWSY GGYMALQMIA KHPNIYRAA IAGGAVSDWR LYDTAYTERY MGYPLEEHVY GASSITGLVE KLPDEPNRLM LVHGLMDENV HFAHLTHLVD ECIKKGKWHE LVIFPNERH GVRNNDASIY LDARMMYFAQ QAIQGFGPTT AAPRQGPLWS HPQFEK

UniProtKB: Dipeptidyl Peptidase Four (IV) family

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223429
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

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

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