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- EMDB-30041: ACE2-B0AT1 complex, open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-30041
TitleACE2-B0AT1 complex, open conformation
Map datacryo-EM map of ACE2-B0AT1 complex, open conformation
Sample
  • Complex: ACE2-B0AT1 complex
    • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
    • Protein or peptide: Angiotensin-converting enzyme 2
Function / homology
Function and homology information


Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / amino acid transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter activity / amino acid transport / positive regulation of amino acid transport / angiotensin-converting enzyme 2 ...Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / amino acid transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter activity / amino acid transport / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / sodium ion transmembrane transport / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / response to nutrient / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Neutral amino acid SLC6 transporter / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. ...Neutral amino acid SLC6 transporter / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Sodium-dependent neutral amino acid transporter B(0)AT1 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYan RH / Zhang YY / Li YN / Xia L / Zhou Q
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Science / Year: 2020
Title: Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
Authors: Renhong Yan / Yuanyuan Zhang / Yaning Li / Lu Xia / Yingying Guo / Qiang Zhou /
Abstract: Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious ...Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious coronavirus disease 2019 (COVID-19) epidemic. Here, we present cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter BAT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 angstroms at the ACE2-RBD interface. The ACE2-BAT1 complex is assembled as a dimer of heterodimers, with the collectrin-like domain of ACE2 mediating homodimerization. The RBD is recognized by the extracellular peptidase domain of ACE2 mainly through polar residues. These findings provide important insights into the molecular basis for coronavirus recognition and infection.
History
DepositionFeb 25, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateApr 8, 2020-
Current statusApr 8, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m1d
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30041.png

Downloads & links

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Map

FileDownload / File: emd_30041.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of ACE2-B0AT1 complex, open conformation
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.32006037 - 1.1108376
Average (Standard dev.)0.0034690418 (±0.054227147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z313.056313.056313.056
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ336336336
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3201.1110.003

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Supplemental data

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Sample components

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Entire : ACE2-B0AT1 complex

EntireName: ACE2-B0AT1 complex
Components
  • Complex: ACE2-B0AT1 complex
    • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
    • Protein or peptide: Angiotensin-converting enzyme 2

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Supramolecule #1: ACE2-B0AT1 complex

SupramoleculeName: ACE2-B0AT1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Sodium-dependent neutral amino acid transporter B(0)AT1

MacromoleculeName: Sodium-dependent neutral amino acid transporter B(0)AT1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.289359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RVRLVLPNPG LDARIPSLAE LETIEQEEAS SRPKWDNKAQ YMLTCLGFCV GLGNVWRFPY LCQSHGGGA FMIPFLILLV LEGIPLLYLE FAIGQRLRRG SLGVWSSIHP ALKGLGLASM LTSFMVGLYY NTIISWIMWY L FNSFQEPL ...String:
MADYKDDDDK SGPDEVDASG RVRLVLPNPG LDARIPSLAE LETIEQEEAS SRPKWDNKAQ YMLTCLGFCV GLGNVWRFPY LCQSHGGGA FMIPFLILLV LEGIPLLYLE FAIGQRLRRG SLGVWSSIHP ALKGLGLASM LTSFMVGLYY NTIISWIMWY L FNSFQEPL PWSDCPLNEN QTGYVDECAR SSPVDYFWYR ETLNISTSIS DSGSIQWWML LCLACAWSVL YMCTIRGIET TG KAVYITS TLPYVVLTIF LIRGLTLKGA TNGIVFLFTP NVTELAQPDT WLDAGAQVFF SFSLAFGGLI SFSSYNSVHN NCE KDSVIV SIINGFTSVY VAIVVYSVIG FRATQRYDDC FSTNILTLIN GFDLPEGNVT QENFVDMQQR CNASDPAAYA QLVF QTCDI NAFLSEAVEG TGLAFIVFTE AITKMPLSPL WSVLFFIMLF CLGLSSMFGN MEGVVVPLQD LRVIPPKWPK EVLTG LICL GTFLIGFIFT LNSGQYWLSL LDSYAGSIPL LIIAFCEMFS VVYVYGVDRF NKDIEFMIGH KPNIFWQVTW RVVSPL LML IIFLFFFVVE VSQELTYSIW DPGYEEFPKS QKISYPNWVY VVVVIVAGVP SLTIPGYAIY KLIRNHCQKP GDHQGLV ST LSTASMNGDL KY

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Macromolecule #2: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.756062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRSSSSWLLL SLVAVTAAWS HPQFEKQSTI EEQAKTFLDK FNHEAEDLFY QSSLASWNYN TNITEENVQN MNNAGDKWSA FLKEQSTLA QMYPLQEIQN LTVKLQLQAL QQNGSSVLSE DKSKRLNTIL NTMSTIYSTG KVCNPDNPQE CLLLEPGLNE I MANSLDYN ...String:
MRSSSSWLLL SLVAVTAAWS HPQFEKQSTI EEQAKTFLDK FNHEAEDLFY QSSLASWNYN TNITEENVQN MNNAGDKWSA FLKEQSTLA QMYPLQEIQN LTVKLQLQAL QQNGSSVLSE DKSKRLNTIL NTMSTIYSTG KVCNPDNPQE CLLLEPGLNE I MANSLDYN ERLWAWESWR SEVGKQLRPL YEEYVVLKNE MARANHYEDY GDYWRGDYEV NGVDGYDYSR GQLIEDVEHT FE EIKPLYE HLHAYVRAKL MNAYPSYISP IGCLPAHLLG DMWGRFWTNL YSLTVPFGQK PNIDVTDAMV DQAWDAQRIF KEA EKFFVS VGLPNMTQGF WENSMLTDPG NVQKAVCHPT AWDLGKGDFR ILMCTKVTMD DFLTAHHEMG HIQYDMAYAA QPFL LRNGA NEGFHEAVGE IMSLSAATPK HLKSIGLLSP DFQEDNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFKG EIPKD QWMK KWWEMKREIV GVVEPVPHDE TYCDPASLFH VSNDYSFIRY YTRTLYQFQF QEALCQAAKH EGPLHKCDIS NSTEAG QKL FNMLRLGKSE PWTLALENVV GAKNMNVRPL LNYFEPLFTW LKDQNKNSFV GWSTDWSPYA DQSIKVRISL KSALGDK AY EWNDNEMYLF RSSVAYAMRQ YFLKVKNQMI LFGEEDVRVA NLKPRISFNF FVTAPKNVSD IIPRTEVEKA IRMSRSRI N DAFRLNDNSL EFLGIQPTLG PPNQPPVSIW LIVFGVVMGV IVVGIVILIF TGIRDRKKKN KARSGENPYA SIDISKGEN NPGFQNTDDV QTSF

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2.14) / Number images used: 143857

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