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- EMDB-36683: Cryo-EM structure of apo-state huamn angiotensin-converting enzym... -

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Basic information

Entry
Database: EMDB / ID: EMD-36683
TitleCryo-EM structure of apo-state huamn angiotensin-converting enzyme 2 (ACE2)
Map dataFinal reconstruction
Sample
  • Complex: Human angiotensin-converting enzyme 2 (ACE2)
    • Protein or peptide: Processed angiotensin-converting enzyme 2
KeywordsReceptor / SARS-Cov-2 / Viral infection / HYDROLASE
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / regulation of transmembrane transporter activity / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / cell surface / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsYang Z / Wang HW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31825009 China
CitationJournal: Nat Methods / Year: 2024
Title: Electrospray-assisted cryo-EM sample preparation to mitigate interfacial effects.
Authors: Zi Yang / Jingjin Fan / Jia Wang / Xiao Fan / Zheng Ouyang / Hong-Wei Wang / Xiaoyu Zhou /
Abstract: Addressing interfacial effects during specimen preparation in cryogenic electron microscopy remains challenging. Here we introduce ESI-cryoPrep, a specimen preparation method based on electrospray ...Addressing interfacial effects during specimen preparation in cryogenic electron microscopy remains challenging. Here we introduce ESI-cryoPrep, a specimen preparation method based on electrospray ionization in native mass spectrometry, designed to alleviate issues associated with protein denaturation or preferred orientation induced by macromolecule adsorption at interfaces. Through fine-tuning spraying parameters, we optimized protein integrity preservation and achieved the desired ice thickness for analyzing target macromolecules. With ESI-cryoPrep, we prepared high-quality cryo-specimens of five proteins and obtained three-dimensional reconstructions at near-atomic resolution. Our findings demonstrate that ESI-cryoPrep effectively confines macromolecules within the middle of the thin layer of amorphous ice, facilitating the preparation of blotting-free vitreous samples. The protective mechanism, characterized by the uneven distribution of charged biomolecules of varying sizes within charged droplets, prevents the adsorption of target biomolecules at air-water or graphene-water interfaces, thereby avoiding structural damage to the protein particles or the introduction of dominant orientation issues.
History
DepositionJun 29, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36683.png

Downloads & links

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Map

FileDownload / File: emd_36683.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 200 pix.
= 167.48 Å		0.84 Å/pix.
x 200 pix.
= 167.48 Å		0.84 Å/pix.
x 200 pix.
= 167.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.058323286 - 0.09831812
Average (Standard dev.)0.00019862218 (±0.0026302352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 167.48001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half1 map of ACE2

Fileemd_36683_half_map_1.map
AnnotationHalf1 map of ACE2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2 map of ACE2

Fileemd_36683_half_map_2.map
AnnotationHalf2 map of ACE2
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 angiotensin-converting enzyme 2 (ACE2)

EntireName: Human angiotensin-converting enzyme 2 (ACE2)
Components
  • Complex: Human angiotensin-converting enzyme 2 (ACE2)
    • Protein or peptide: Processed angiotensin-converting enzyme 2

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Supramolecule #1: Human angiotensin-converting enzyme 2 (ACE2)

SupramoleculeName: Human angiotensin-converting enzyme 2 (ACE2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.94 kDa/nm

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.153664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL ...String:
STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL KNEMARANHY EDYGDYWRGD YEVNGVDGYD YSRGQLIEDV EHTFEEIKPL YEHLHAYVRA KLMNAYPSYI SP IGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD AMVDQAWDAQ RIFKEAEKFF VSVGLPNMTQ GFWENSMLTD PGN VQKAVC HPTAWDLGKG DFRILMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LSPDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVSNDYSF IRYYTRTLYQ FQFQEALCQA AKHEGPLHKC DISNSTEAGQ KLFNMLRLGK SEPWTLALEN VVGAKN MNV RPLLNYFEPL FTWLKDQNKN SFVGWSTDWS PYAD

UniProtKB: Angiotensin-converting enzyme 2

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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

Concentration0.88 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMCH3COONH4Ammonium acetate
20.0 mMC4H11NO3Tris

Details: The main salt in buffer should be volatile.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: AIR
Details: The chamber was air-pumped by a suction pump for 2 minutes.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 284 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification carried out through ESI-cryoPrep method..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 95.0 K / Max: 102.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4090 pixel / Number grids imaged: 1 / Number real images: 1000 / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.786 µm / Calibrated defocus min: 0.492 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected micrographs were motion-corrected and CTF estimated.
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1r42

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121524
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial local fitting was done with a deep-learning based software cryonet.
RefinementProtocol: OTHER / Overall B value: 83.57
Output model

PDB-8jwh:
Cryo-EM structure of apo-state huamn angiotensin-converting enzyme 2 (ACE2)

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