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- EMDB-66669: Structure of the human aminopeptidase N (CD13) ectodomain -

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Basic information

Entry
Database: EMDB / ID: EMD-66669
TitleStructure of the human aminopeptidase N (CD13) ectodomain
Map data
Sample
  • Complex: Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHCoV-229E spike protein receptor / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLiang J / Li S
Funding support China, 3 items
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, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66669.png

Downloads & links

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Map

FileDownload / File: emd_66669.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.9796952 - 1.5334959
Average (Standard dev.)0.0011590888 (±0.055301808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 240.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66669_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66669_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66669_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag

EntireName: Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag
Components
  • Complex: Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag

SupramoleculeName: Human aminopeptidase N protein ectodomain fused to C-terminal Fc tag
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aminopeptidase N

MacromoleculeName: Aminopeptidase N / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: membrane alanyl aminopeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.153617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DQSKAWNRYR LPNTLKPDSY RVTLRPYLTP NDRGLYVFKG SSTVRFTCKE ATDVIIIHSK KLNYTLSQGH RVVLRGVGGS QPPDIDKTE LVEPTEYLVV HLKGSLVKDS QYEMDSEFEG ELADDLAGFY RSEYMEGNVR KVVATTQMQA ADARKSFPCF D EPAMKAEF ...String:
DQSKAWNRYR LPNTLKPDSY RVTLRPYLTP NDRGLYVFKG SSTVRFTCKE ATDVIIIHSK KLNYTLSQGH RVVLRGVGGS QPPDIDKTE LVEPTEYLVV HLKGSLVKDS QYEMDSEFEG ELADDLAGFY RSEYMEGNVR KVVATTQMQA ADARKSFPCF D EPAMKAEF NITLIHPKDL TALSNMLPKG PSTPLPEDPN WNVTEFHTTP KMSTYLLAFI VSEFDYVEKQ ASNGVLIRIW AR PSAIAAG HGDYALNVTG PILNFFAGHY DTPYPLPKSD QIGLPDFNAG AMENWGLVTY RENSLLFDPL SSSSSNKERV VTV IAHELA HQWFGNLVTI EWWNDLWLNE GFASYVEYLG ADYAEPTWNL KDLMVLNDVY RVMAVDALAS SHPLSTPASE INTP AQISE LFDAISYSKG ASVLRMLSSF LSEDVFKQGL ASYLHTFAYQ NTIYLNLWDH LQEAVNNRSI QLPTTVRDIM NRWTL QMGF PVITVDTSTG TLSQEHFLLD PDSNVTRPSE FNYVWIVPIT SIRDGRQQQD YWLIDVRAQN DLFSTSGNEW VLLNLN VTG YYRVNYDEEN WRKIQTQLQR DHSAIPVINR AQIINDAFNL ASAHKVPVTL ALNNTLFLIE ERQYMPWEAA LSSLSYF KL MFDRSEVYGP MKNYLKKQVT PLFIHFRNNT NNWREIPENL MDQYSEVNAI STACSNGVPE CEEMVSGLFK QWMENPNN N PIHPNLRSTV YCNAIAQGGE EEWDFAWEQF RNATLVNEAD KLRAALACSK ELWILNRYLS YTLNPDLIRK QDATSTIIS ITNNVIGQGL VWDFVQSNWK KLFNDYGGGS FSFSNLIQAV TRRFSTEYEL QQLEQFKKDN EETGFGSGTR ALEQALEKTK ANIKWVKEN KEVVLQWFTE NSK

UniProtKB: Aminopeptidase N

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 20 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm

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Image processing

Particle selectionNumber selected: 146162
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 72577
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.6.0)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: predicted by CryoNet
Output model

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

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