+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17582 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo) | |||||||||||||||
Map data | Full map processed with LocScale. | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | Dipeptidylpeptidase / HYDROLASE | |||||||||||||||
Function / homology | Function and homology information dipeptidyl-peptidase activity / serine-type peptidase activity / proteolysis Similarity search - Function | |||||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||||||||
Authors | Gudipati RK / Cavadini S / Kempf G / Grosshans H | |||||||||||||||
Funding support | Switzerland, Poland, 4 items
| |||||||||||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of Caenorhabditis elegans DPF-3 (apo) Authors: Gudipati RK / Cavadini S / Kempf G / Grosshans H | |||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17582.map.gz | 41.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17582-v30.xml emd-17582.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17582_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_17582.png | 119.2 KB | ||
Filedesc metadata | emd-17582.cif.gz | 5.8 KB | ||
Others | emd_17582_additional_1.map.gz emd_17582_half_map_1.map.gz emd_17582_half_map_2.map.gz | 64 MB 64.1 MB 64.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17582 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17582 | HTTPS FTP |
-Validation report
Summary document | emd_17582_validation.pdf.gz | 751.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_17582_full_validation.pdf.gz | 751.1 KB | Display | |
Data in XML | emd_17582_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | emd_17582_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17582 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17582 | HTTPS FTP |
-Related structure data
Related structure data | 8pbaMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_17582.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full map processed with LocScale. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.845 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Full map.
File | emd_17582_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2.
File | emd_17582_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1.
File | emd_17582_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Homodimeric complex of DPF-3
Entire | Name: Homodimeric complex of DPF-3 |
---|---|
Components |
|
-Supramolecule #1: Homodimeric complex of DPF-3
Supramolecule | Name: Homodimeric complex of DPF-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
-Macromolecule #1: Dipeptidyl Peptidase Four (IV) family
Macromolecule | Name: Dipeptidyl Peptidase Four (IV) family / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Molecular weight | Theoretical: 106.462812 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
---|---|
Output model | PDB-8pba: |