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- EMDB-26350: Cryo-EM Structure of DNPEP -

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Basic information

Entry
Database: EMDB / ID: EMD-26350
TitleCryo-EM Structure of DNPEP
Map data
Sample
  • Complex: Dodecamer of Aspartyl Aminopeptidase
    • Protein or peptide: Aspartyl aminopeptidase
  • Ligand: ZINC ION
KeywordsDNPEP / aminopeptidase / tetrahedral Symmetry / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


aspartyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Aspartyl aminopeptidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsMorgan CE / Yu EW / Zhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2022
Title: Toward structural-omics of the bovine retinal pigment epithelium.
Authors: Christopher E Morgan / Zhemin Zhang / Masaru Miyagi / Marcin Golczak / Edward W Yu /
Abstract: The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on ...The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
History
DepositionMar 2, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26350.png

Downloads & links

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Map

FileDownload / File: emd_26350.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0170722 - 1.5373739
Average (Standard dev.)0.00004978191 (±0.06490438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26350_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_26350_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_26350_half_map_2.map
Projections & Slices
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Sample components

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Entire : Dodecamer of Aspartyl Aminopeptidase

EntireName: Dodecamer of Aspartyl Aminopeptidase
Components
  • Complex: Dodecamer of Aspartyl Aminopeptidase
    • Protein or peptide: Aspartyl aminopeptidase
  • Ligand: ZINC ION

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Supramolecule #1: Dodecamer of Aspartyl Aminopeptidase

SupramoleculeName: Dodecamer of Aspartyl Aminopeptidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Aspartyl aminopeptidase

MacromoleculeName: Aspartyl aminopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: aspartyl aminopeptidase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 51.893188 KDa
SequenceString: MSGRARKEAV QAAARELLKF VNRSPSPFHA VAECRSRLLQ AGFHELKETE SWDIKPESKY FLTRNSSTII AFAVGGQYVP GNGFSLIGA HTDSPCLRVK RRSRRSQVGF QQVGVETYGG GIWSTWFDRD LTLAGRVIVK CPTSGRLEQR LVHVDRPILR I PHLAIHLQ ...String:
MSGRARKEAV QAAARELLKF VNRSPSPFHA VAECRSRLLQ AGFHELKETE SWDIKPESKY FLTRNSSTII AFAVGGQYVP GNGFSLIGA HTDSPCLRVK RRSRRSQVGF QQVGVETYGG GIWSTWFDRD LTLAGRVIVK CPTSGRLEQR LVHVDRPILR I PHLAIHLQ RNVNENFGPN MEMHLVPILA TSIQEELEKG TPEPGPLNAT DERHHSVLTS LLCAHLGLSP EDILEMELCL AD TQPAVLG GAYEEFIFAP RLDNLHSCFC ALQALIDSCS APASLAADPH VRMIALYDNE EVGSESAQGA QSLLTELVLR RIS ASPQHL TAFEEAIPKS YMISADMAHA VHPNYLDKHE ENHRPLFHKG PVIKVNSKQR YASNAVSEAL IREVASSVGV PLQD LMVRN DSPCGTTIGP ILASRLGLRV LDLGSPQLAM HSIRETACTT GVLQTITLFK GFFELFPSLS RSLLVD

UniProtKB: Aspartyl aminopeptidase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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 reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 629
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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