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- EMDB-45396: Aminopeptidase N close state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45396
TitleAminopeptidase N close state
Map dataAminopeptidase N close state
Sample
  • Complex: Aminopeptidase N
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
Keywordshuman / kidney / Aminopeptidase N / MEMBRANE PROTEIN / HYDROLASE
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane ...alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane / metallopeptidase activity / signaling receptor activity / virus receptor activity / angiogenesis / cell differentiation / lysosomal membrane / external side of plasma membrane / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm
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: 2.96 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: Aminopeptidase N close state
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_45396.png

Downloads & links

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Map

FileDownload / File: emd_45396.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAminopeptidase N close state
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: 0.15
Minimum - Maximum-0.5344844 - 1.0673962
Average (Standard dev.)-0.00063940993 (±0.033477325)
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 B

Fileemd_45396_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_45396_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aminopeptidase N

EntireName: Aminopeptidase N
Components
  • Complex: Aminopeptidase N
    • Protein or peptide: Aminopeptidase N
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Aminopeptidase N

SupramoleculeName: Aminopeptidase N / 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: 109.641078 KDa
SequenceString: MAKGFYISKS LGILGILLGV AAVCTIIALS VVYSQEKNKN ANSSPVASTT PSASATTNPA SATTLDQSKA WNRYRLPNTL KPDSYRVTL RPYLTPNDRG LYVFKGSSTV RFTCKEATDV IIIHSKKLNY TLSQGHRVVL RGVGGSQPPD IDKTELVEPT E YLVVHLKG ...String:
MAKGFYISKS LGILGILLGV AAVCTIIALS VVYSQEKNKN ANSSPVASTT PSASATTNPA SATTLDQSKA WNRYRLPNTL KPDSYRVTL RPYLTPNDRG LYVFKGSSTV RFTCKEATDV IIIHSKKLNY TLSQGHRVVL RGVGGSQPPD IDKTELVEPT E YLVVHLKG SLVKDSQYEM DSEFEGELAD DLAGFYRSEY MEGNVRKVVA TTQMQAADAR KSFPCFDEPA MKAEFNITLI HP KDLTALS NMLPKGPSTP LPEDPNWNVT EFHTTPKMST YLLAFIVSEF DYVEKQASNG VLIRIWARPS AIAAGHGDYA LNV TGPILN FFAGHYDTPY PLPKSDQIGL PDFNAGAMEN WGLVTYRENS LLFDPLSSSS SNKERVVTVI AHELAHQWFG NLVT IEWWN DLWLNEGFAS YVEYLGADYA EPTWNLKDLM VLNDVYRVMA VDALASSHPL STPASEINTP AQISELFDAI SYSKG ASVL RMLSSFLSED VFKQGLASYL HTFAYQNTIY LNLWDHLQEA VNNRSIQLPT TVRDIMNRWT LQMGFPVITV DTSTGT LSQ EHFLLDPDSN VTRPSEFNYV WIVPITSIRD GRQQQDYWLI DVRAQNDLFS TSGNEWVLLN LNVTGYYRVN YDEENWR KI QTQLQRDHSA IPVINRAQII NDAFNLASAH KVPVTLALNN TLFLIEERQY MPWEAALSSL SYFKLMFDRS EVYGPMKN Y LKKQVTPLFI HFRNNTNNWR EIPENLMDQY SEVNAISTAC SNGVPECEEM VSGLFKQWME NPNNNPIHPN LRSTVYCNA IAQGGEEEWD FAWEQFRNAT LVNEADKLRA ALACSKELWI LNRYLSYTLN PDLIRKQDAT STIISITNNV IGQGLVWDFV QSNWKKLFN DYGGGSFSFS NLIQAVTRRF STEYELQQLE QFKKDNEETG FGSGTRALEQ ALEKTKANIK WVKENKEVVL Q WFTENSK

UniProtKB: Aminopeptidase N

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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: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / 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

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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15546
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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