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- PDB-9x9k: Structure of the human aminopeptidase N (CD13) ectodomain -

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Basic information

Entry
Database: PDB / ID: 9x9k
TitleStructure of the human aminopeptidase N (CD13) ectodomain
ComponentsAminopeptidase N
KeywordsHYDROLASE / HCoV-229E spike protein receptor
Function / homology
Function and homology information


membrane alanyl aminopeptidase / alanyl aminopeptidase activity / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / secretory granule membrane / metallopeptidase activity ...membrane alanyl aminopeptidase / alanyl aminopeptidase activity / peptide catabolic process / metalloaminopeptidase activity / endoplasmic reticulum-Golgi intermediate compartment / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / secretory granule membrane / metallopeptidase activity / signaling receptor activity / external side of plasma membrane / lysosomal membrane / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy ...Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLiang, J. / Li, S.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241031 China
National Natural Science Foundation of China (NSFC)32171195 China
National Natural Science Foundation of China (NSFC)82241066 China
CitationJournal: To Be Published
Title: Cryo-ET analysis of the modulation of the spike protein in alphacoronavirus by temperature and receptor
Authors: Liang, J. / Peng, C. / Zhang, Z. / Song, Y. / Li, S.
History
DepositionOct 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase N
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,73122
Polymers206,3072
Non-polymers4,42420
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Aminopeptidase N / AP-N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid ...AP-N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 103153.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP, APN, CD13, PEPN / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P15144, membrane alanyl aminopeptidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
11cryoSPARC4.6.0classification
12cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 146162
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72577 / Symmetry type: POINT
Atomic model buildingDetails: predicted by CryoNet / Source name: Other / Type: in silico model

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