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- EMDB-46579: Apo ACE full dimer 1 prepared by chameleon -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46579
TitleApo ACE full dimer 1 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 / positive regulation of peptidyl-cysteine S-nitrosylation ...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 / positive regulation of peptidyl-cysteine S-nitrosylation / negative regulation of calcium ion import / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / hormone catabolic process / bradykinin catabolic process / cellular response to aldosterone / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of D-glucose import / vasoconstriction / regulation of smooth muscle cell migration / neutrophil mediated immunity / regulation of hematopoietic stem cell proliferation / hormone metabolic process / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / arachidonate secretion / post-transcriptional regulation of gene expression / eating behavior / heterocyclic compound binding / peptide catabolic process / lung alveolus development / heart contraction / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of systemic arterial blood pressure / response to dexamethasone / 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 / regulation of vasoconstriction / animal organ regeneration / peptidyl-dipeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of vasoconstriction / sperm midpiece / blood vessel diameter maintenance / basal plasma membrane / kidney development / angiotensin-activated signaling pathway / female pregnancy / brush border membrane / response to nutrient levels / cellular response to glucose stimulus / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / lysosome / calmodulin binding / endosome / positive regulation of apoptotic process / response to xenobiotic stimulus / external side of plasma membrane / negative regulation of gene expression / 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: 3.05 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
CitationJournal: 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 13, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46579.png

Downloads & links

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Map

FileDownload / File: emd_46579.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.45543274 - 0.6754376
Average (Standard dev.)0.0003871232 (±0.016546095)
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_46579_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46579_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 : 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: 6 / 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51497
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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