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- EMDB-30888: Conformation 1 of S-ACE2-B0AT1 ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30888
TitleConformation 1 of S-ACE2-B0AT1 ternary complex
Map data
SampleConformation 1 of S-ACE2-B0AT1 ternary complex
  • Sodium-dependent neutral amino acid transporter B(0)AT1
  • Angiotensin-converting enzyme 2
  • Spike glycoproteinPeplomer
  • (ligand) x 4
Function / homology
Function and homology information


neutral amino acid transmembrane transporter activity / positive regulation of amino acid transport / positive regulation of L-proline import across plasma membrane / angiotensin-converting enzyme 2 / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / amino acid transport ...neutral amino acid transmembrane transporter activity / positive regulation of amino acid transport / positive regulation of L-proline import across plasma membrane / angiotensin-converting enzyme 2 / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / amino acid transport / regulation of systemic arterial blood pressure by renin-angiotensin / symporter activity / peptidyl-dipeptidase activity / regulation of vasoconstriction / blood vessel diameter maintenance / angiotensin maturation / sodium ion transmembrane transport / carboxypeptidase activity / brush border membrane / metallocarboxypeptidase activity / regulation of cytokine production / negative regulation of signaling receptor activity / regulation of cardiac conduction / regulation of transmembrane transporter activity / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / response to nutrient / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / metallopeptidase activity / regulation of cell population proliferation / viral translation / virus receptor activity / positive regulation of reactive oxygen species metabolic process / host cell surface receptor binding / endocytosis involved in viral entry into host cell / regulation of inflammatory response / endocytic vesicle membrane / endopeptidase activity / apical plasma membrane / fusion of virus membrane with host plasma membrane / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / membrane raft / go:0009405: / proteolysis / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / cell surface / integral component of plasma membrane / extracellular space / extracellular exosome / zinc ion binding / integral component of membrane / extracellular region / identical protein binding / plasma membrane
Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Collectrin domain / Spike receptor binding domain superfamily, coronavirus / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Sodium:neurotransmitter symporter superfamily / Spike glycoprotein, betacoronavirus / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S1, C-terminal ...Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Collectrin domain / Spike receptor binding domain superfamily, coronavirus / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Sodium:neurotransmitter symporter superfamily / Spike glycoprotein, betacoronavirus / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Neutral amino acid SLC6 transporter / Peptidase M2, peptidyl-dipeptidase A / Sodium:neurotransmitter symporter
Spike glycoprotein / Sodium-dependent neutral amino acid transporter B(0)AT1 / Angiotensin-converting enzyme 2
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsYan RH / Zhang YY / Li YN / Ye FF / Guo YY / Xia L / Zhong XY / Chi XM / 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)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Res / Year: 2021
Title: Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2.
Authors: Renhong Yan / Yuanyuan Zhang / Yaning Li / Fangfei Ye / Yingying Guo / Lu Xia / Xinyue Zhong / Ximin Chi / Qiang Zhou /
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJan 18, 2021-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing 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
  • Download
  • 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-7dwx
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dwx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30888.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 480 pix.
= 521.76 Å
1.09 Å/pix.
x 480 pix.
= 521.76 Å
1.09 Å/pix.
x 480 pix.
= 521.76 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
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.8685004 - 1.7861811
Average (Standard dev.)0.009391131 (±0.07414661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 521.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z521.760521.760521.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.8691.7860.009

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Supplemental data

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Sample components

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Entire Conformation 1 of S-ACE2-B0AT1 ternary complex

EntireName: Conformation 1 of S-ACE2-B0AT1 ternary complex / Number of components: 8

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Component #1: protein, Conformation 1 of S-ACE2-B0AT1 ternary complex

ProteinName: Conformation 1 of S-ACE2-B0AT1 ternary complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Sodium-dependent neutral amino acid transporter B(0)AT1

ProteinName: Sodium-dependent neutral amino acid transporter B(0)AT1
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 73.289359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Angiotensin-converting enzyme 2

ProteinName: Angiotensin-converting enzyme 2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 93.971266 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 142.502594 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 64 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #6: ligand, LEUCINE

LigandName: LEUCINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.131173 kDa

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Component #7: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #8: ligand, water

LigandName: water / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 53141
3D reconstructionSoftware: cryoSPARC / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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