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- EMDB-45401: human kidney Dipeptidyl peptidase 4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45401
Titlehuman kidney Dipeptidyl peptidase 4
Map datahuman kidney Dipeptidyl peptidase 4
Sample
  • Complex: Dipeptidyl peptidase 4
    • Protein or peptide: Dipeptidyl peptidase 4 membrane form
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshuman / kidney / Dipeptidyl peptidase 4 / MEMBRANE PROTEIN
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / chemorepellent activity / psychomotor behavior / intercellular canaliculus / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / chemorepellent activity / psychomotor behavior / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / T cell costimulation / receptor-mediated endocytosis of virus by host cell / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / membrane fusion / response to hypoxia / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / membrane raft / signaling receptor binding / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / symbiont entry into host cell / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLyu M / Zhang Z / Tringides M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: human kidney Dipeptidyl peptidase 4
Authors: Lyu M / Zhang Z
History
DepositionJun 17, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45401.png

Downloads & links

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Map

FileDownload / File: emd_45401.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman kidney Dipeptidyl peptidase 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4596951 - 0.97166187
Average (Standard dev.)-0.0005337537 (±0.026117528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_45401_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_45401_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dipeptidyl peptidase 4

EntireName: Dipeptidyl peptidase 4
Components
  • Complex: Dipeptidyl peptidase 4
    • Protein or peptide: Dipeptidyl peptidase 4 membrane form
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Dipeptidyl peptidase 4

SupramoleculeName: Dipeptidyl peptidase 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dipeptidyl peptidase 4 membrane form

MacromoleculeName: Dipeptidyl peptidase 4 membrane form / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.367281 KDa
SequenceString: MKTPWKVLLG LLGAAALVTI ITVPVVLLNK GTDDATADSR KTYTLTDYLK NTYRLKLYSL RWISDHEYLY KQENNILVFN AEYGNSSVF LENSTFDEFG HSINDYSISP DGQFILLEYN YVKQWRHSYT ASYDIYDLNK RQLITEERIP NNTQWVTWSP V GHKLAYVW ...String:
MKTPWKVLLG LLGAAALVTI ITVPVVLLNK GTDDATADSR KTYTLTDYLK NTYRLKLYSL RWISDHEYLY KQENNILVFN AEYGNSSVF LENSTFDEFG HSINDYSISP DGQFILLEYN YVKQWRHSYT ASYDIYDLNK RQLITEERIP NNTQWVTWSP V GHKLAYVW NNDIYVKIEP NLPSYRITWT GKEDIIYNGI TDWVYEEEVF SAYSALWWSP NGTFLAYAQF NDTEVPLIEY SF YSDESLQ YPKTVRVPYP KAGAVNPTVK FFVVNTDSLS SVTNATSIQI TAPASMLIGD HYLCDVTWAT QERISLQWLR RIQ NYSVMD ICDYDESSGR WNCLVARQHI EMSTTGWVGR FRPSEPHFTL DGNSFYKIIS NEEGYRHICY FQIDKKDCTF ITKG TWEVI GIEALTSDYL YYISNEYKGM PGGRNLYKIQ LSDYTKVTCL SCELNPERCQ YYSVSFSKEA KYYQLRCSGP GLPLY TLHS SVNDKGLRVL EDNSALDKML QNVQMPSKKL DFIILNETKF WYQMILPPHF DKSKKYPLLL DVYAGPCSQK ADTVFR LNW ATYLASTENI IVASFDGRGS GYQGDKIMHA INRRLGTFEV EDQIEAARQF SKMGFVDNKR IAIWGWSYGG YVTSMVL GS GSGVFKCGIA VAPVSRWEYY DSVYTERYMG LPTPEDNLDH YRNSTVMSRA ENFKQVEYLL IHGTADDNVH FQQSAQIS K ALVDVGVDFQ AMWYTDEDHG IASSTAHQHI YTHMSHFIKQ CFSLP

UniProtKB: Dipeptidyl peptidase 4

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11336
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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