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- EMDB-46581: Apo ACE full dimer 3 prepared by chameleon -

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Basic information

Entry
Database: EMDB / ID: EMD-46581
TitleApo ACE full dimer 3 prepared by chameleon
Map data
Sample
  • Complex: Angiotensin I converting enzyme homodimer
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshomodimer / zinc metalloprotease / HYDROLASE
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / tripeptidyl-peptidase activity / peptidyl-dipeptidase A / regulation of renal output by angiotensin / negative regulation of gap junction assembly / hormone catabolic process / bradykinin catabolic process / metallodipeptidase activity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / neutrophil mediated immunity / hormone metabolic process / mitogen-activated protein kinase binding / mitogen-activated protein kinase kinase binding / chloride ion binding / arachidonate secretion / post-transcriptional regulation of gene expression / peptide catabolic process / heart contraction / positive regulation of systemic arterial blood pressure / antigen processing and presentation of peptide antigen via MHC class I / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / amyloid-beta metabolic process / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / regulation of vasoconstriction / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / blood vessel diameter maintenance / angiotensin-activated signaling pathway / kidney development / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / calmodulin binding / lysosome / endosome / negative regulation of gene expression / external side of plasma membrane / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsMancl JM / Tang WJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Elife / Year: 2025
Title: Dimerization and dynamics of human angiotensin-I converting enzyme revealed by cryo-EM and MD simulations.
Authors: Jordan M Mancl / Xiaoyang Wu / Minglei Zhao / Wei-Jen Tang /
Abstract: Angiotensin-I converting enzyme (ACE) regulates the levels of disparate bioactive peptides, notably converting angiotensin-I to angiotensin-II and degrading amyloid beta. ACE is a heavily ...Angiotensin-I converting enzyme (ACE) regulates the levels of disparate bioactive peptides, notably converting angiotensin-I to angiotensin-II and degrading amyloid beta. ACE is a heavily glycosylated dimer, containing four analogous catalytic sites, and exists in membrane-bound and soluble (sACE) forms. ACE inhibition is a frontline, FDA-approved, therapy for cardiovascular diseases yet is associated with significant side effects, including higher rates of lung cancer. To date, structural studies have been confined to individual domains or partially denatured cryo-EM structures. Here, we report the cryo-EM structure of the glycosylated full human sACE dimer. We resolved four structural states at 2.99 - 3.65 Å resolution which are primarily differentiated by varying degrees of solvent accessibility to the active sites and reveal the full dimerization interface. We also employed all-atom molecular dynamics (MD) simulations and heterogeneity analysis in cryoSPARC, cryoDRGN, and RECOVAR to elucidate the conformational dynamics of sACE and identify key regions mediating conformational change. We identify differences in the mechanisms governing the conformational dynamics of individual domains that have implications for the design of domain-specific sACE modulators.
#1: Journal: Elife / Year: 2025
Title: Dimerization and dynamics of angiotensin-I converting enzyme revealed by cryoEM and MD simulations
Authors: Mancl JM / Wu X / Zhao M / Tang WJ
History
DepositionAug 14, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46581.png

Downloads & links

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Map

FileDownload / File: emd_46581.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.4721217 - 0.6428531
Average (Standard dev.)0.00037100905 (±0.015645374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46581_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_46581_half_map_2.map
Projections & Slices
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Sample components

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Entire : Angiotensin I converting enzyme homodimer

EntireName: Angiotensin I converting enzyme homodimer
Components
  • Complex: Angiotensin I converting enzyme homodimer
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Angiotensin I converting enzyme homodimer

SupramoleculeName: Angiotensin I converting enzyme homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: peptidyl-dipeptidase A
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142.804797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAASGRRGP GLLLPLPLLL LLPPQPALAL DPGLQPGNFS ADEAGAQLFA QSYNSSAEQV LFQSVAASWA HDTNITAENA RRQEEAALL SQEFAEAWGQ KAKELYEPIW QNFTDPQLRR IIGAVRTLGS ANLPLAKRQQ YNALLSNMSR IYSTAKVCLP N KTATCWSL ...String:
MGAASGRRGP GLLLPLPLLL LLPPQPALAL DPGLQPGNFS ADEAGAQLFA QSYNSSAEQV LFQSVAASWA HDTNITAENA RRQEEAALL SQEFAEAWGQ KAKELYEPIW QNFTDPQLRR IIGAVRTLGS ANLPLAKRQQ YNALLSNMSR IYSTAKVCLP N KTATCWSL DPDLTNILAS SRSYAMLLFA WEGWHNAAGI PLKPLYEDFT ALSNEAYKQD GFTDTGAYWR SWYNSPTFED DL EHLYQQL EPLYLNLHAF VRRALHRRYG DRYINLRGPI PAHLLGDMWA QSWENIYDMV VPFPDKPNLD VTSTMLQQGW NAT HMFRVA EEFFTSLELS PMPPEFWEGS MLEKPADGRE VVCHASAWDF YNRKDFRIKQ CTRVTMDQLS TVHHEMGHIQ YYLQ YKDLP VSLRRGANPG FHEAIGDVLA LSVSTPEHLH KIGLLDRVTN DTESDINYLL KMALEKIAFL PFGYLVDQWR WGVFS GRTP PSRYNFDWWY LRTKYQGICP PVTRNETHFD AGAKFHVPNV TPYIRYFVSF VLQFQFHEAL CKEAGYEGPL HQCDIY RST KAGAKLRKVL QAGSSRPWQE VLKDMVGLDA LDAQPLLKYF QPVTQWLQEQ NQQNGEVLGW PEYQWHPPLP DNYPEGI DL VTDEAEASKF VEEYDRTSQV VWNEYAEANW NYNTNITTET SKILLQKNMQ IANHTLKYGT QARKFDVNQL QNTTIKRI I KKVQDLERAA LPAQELEEYN KILLDMETTY SVATVCHPNG SCLQLEPDLT NVMATSRKYE DLLWAWEGWR DKAGRAILQ FYPKYVELIN QAARLNGYVD AGDSWRSMYE TPSLEQDLER LFQELQPLYL NLHAYVRRAL HRHYGAQHIN LEGPIPAHLL GNMWAQTWS NIYDLVVPFP SAPSMDTTEA MLKQGWTPRR MFKEADDFFT SLGLLPVPPE FWNKSMLEKP TDGREVVCHA S AWDFYNGK DFRIKQCTTV NLEDLVVAHH EMGHIQYFMQ YKDLPVALRE GANPGFHEAI GDVLALSVST PKHLHSLNLL SS EGGSDEH DINFLMKMAL DKIAFIPFSY LVDQWRWRVF DGSITKENYN QEWWSLRLKY QGLCPPVPRT QGDFDPGAKF HIP SSVPYI RYFVSFIIQF QFHEALCQAA GHTGPLHKCD IYQSKEAGQR LATAMKLGFS RPWPEAMQLI TGQPNMSASA MLSY FKPLL DWLRTENELH GEKLGWPQYN WTPNSARSEG HHHHHH

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / 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: 5.5
VitrificationCryogen name: ETHANE / Details: Grids prepared at NCCAT using Chameleon.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48375
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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