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- EMDB-30039: The 2019-nCoV RBD/ACE2-B0AT1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30039
TitleThe 2019-nCoV RBD/ACE2-B0AT1 complex
Map datacryo EM map of the complex of the ACE2-B0AT1 complex with the RBD of 2019-nCoV
Sample
  • Complex: the SARS-coV-2 RBD/ACE2-B0AT1 complex
    • Complex: the SARS-coV-2 RBD
      • Protein or peptide: Spike protein S1
    • Complex: ACE2-B0AT1
      • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
      • Protein or peptide: Angiotensin-converting enzyme 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LEUCINE
  • Ligand: ZINC ION
  • Ligand: water
Keywords2019-nCoV RBD / ACE2-B0AT1 complex / MEMBRANE PROTEIN / MEMBRANE PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / symporter activity / SLC-mediated transport of neurotransmitters / positive regulation of amino acid transport / amino acid transport ...Defective SLC6A19 causes Hartnup disorder (HND) / Defective SLC6A19 causes Hartnup disorder (HND) / neutral amino acid transport / neutral L-amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / symporter activity / SLC-mediated transport of neurotransmitters / positive regulation of amino acid transport / 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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / viral life cycle / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / response to nutrient / regulation of cytokine production / sodium ion transmembrane transport / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / membrane raft / receptor ligand activity / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / 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 domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A ...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 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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Sodium-dependent neutral amino acid transporter B(0)AT1 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYan RH / Zhang YY
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 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 24, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMar 11, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.66
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m17
  • Surface level: 0.66
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30039.png

Downloads & links

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Map

FileDownload / File: emd_30039.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo EM map of the complex of the ACE2-B0AT1 complex with the RBD of 2019-nCoV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66 / Movie #1: 0.66
Minimum - Maximum-1.8686575 - 3.59318
Average (Standard dev.)0.0061106896 (±0.09984576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin001
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
MAP C/R/S123
start NC/NR/NS001
NC/NR/NS288288288
D min/max/mean-1.8693.5930.006

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Supplemental data

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Sample components

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Entire : the SARS-coV-2 RBD/ACE2-B0AT1 complex

EntireName: the SARS-coV-2 RBD/ACE2-B0AT1 complex
Components
  • Complex: the SARS-coV-2 RBD/ACE2-B0AT1 complex
    • Complex: the SARS-coV-2 RBD
      • Protein or peptide: Spike protein S1
    • Complex: ACE2-B0AT1
      • Protein or peptide: Sodium-dependent neutral amino acid transporter B(0)AT1
      • Protein or peptide: Angiotensin-converting enzyme 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LEUCINE
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: the SARS-coV-2 RBD/ACE2-B0AT1 complex

SupramoleculeName: the SARS-coV-2 RBD/ACE2-B0AT1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: cryo EM map of the complex of 2019-nCoV RBD with the ACE2-B0AT1 complex

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Supramolecule #2: the SARS-coV-2 RBD

SupramoleculeName: the SARS-coV-2 RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Details: cryo EM map of the complex of 2019-nCoV RBD with the ACE2-B0AT1 complex, focused refined on 2019-nCoV RBD
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: ACE2-B0AT1

SupramoleculeName: ACE2-B0AT1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Details: cryo EM map of the complex of 2019-nCoV RBD with the ACE2-B0AT1 complex, focused refined on ACE2-B0AT1
Source (natural)Organism: 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

UniProtKB: Sodium-dependent neutral amino acid transporter B(0)AT1

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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

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #3: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.122336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNF

UniProtKB: Spike glycoprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: LEUCINE

MacromoleculeName: LEUCINE / type: ligand / ID: 7 / Number of copies: 2 / Formula: LEU
Molecular weightTheoretical: 131.173 Da
Chemical component information

ChemComp-LEU:
LEUCINE

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.13.2) / Number images used: 301565
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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