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- EMDB-32176: SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 state -

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Basic information

Entry
Database: EMDB / ID: EMD-32176
TitleSARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 stateCoronavirus spike protein
Map data
SampleSARS-CoV-2 spike protein in complex with ACE2, Beta VariantCoronavirus spike protein
  • SARS-CoV-2 spike proteinCoronavirus spike protein
  • ACE2Angiotensin-converting enzyme 2
  • Spike glycoproteinSpike protein
  • Angiotensin-converting enzyme 2
Function / homology
Function and homology information


positive regulation of amino acid transport / positive regulation of L-proline import across plasma membrane / angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / angiotensin-mediated drinking behavior / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity ...positive regulation of amino acid transport / positive regulation of L-proline import across plasma membrane / angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / angiotensin-mediated drinking behavior / positive regulation of cardiac muscle contraction / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity / regulation of cardiac conduction / regulation of vasoconstriction / blood vessel diameter maintenance / angiotensin maturation / Attachment and Entry / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / metallocarboxypeptidase activity / brush border membrane / regulation of cytokine production / negative regulation of signaling receptor activity / regulation of transmembrane transporter activity / cilium / metallopeptidase activity / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of reactive oxygen species metabolic process / Attachment and Entry / virus receptor activity / receptor-mediated virion attachment to host cell / regulation of cell population proliferation / Potential therapeutics for SARS / endoplasmic reticulum-Golgi intermediate compartment / regulation of inflammatory response / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / endopeptidase activity / apical plasma membrane / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral entry into host cell / viral envelope / membrane raft / proteolysis / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / integral component of membrane / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsXu C / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2021
Title: Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Authors: Yifan Wang / Cong Xu / Yanxing Wang / Qin Hong / Chao Zhang / Zuyang Li / Shiqi Xu / Qinyu Zuo / Caixuan Liu / Zhong Huang / Yao Cong /
Abstract: The emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 ...The emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 pandemic. Understanding the structural nature of Kappa and Beta spike (S) proteins and their association with ACE2 is of significant importance. Here we present two cryo-EM structures for each of the Kappa and Beta spikes in the open and open-prone transition states. Compared with wild-type (WT) or G614 spikes, the two variant spikes appear more untwisted/open especially for Beta, and display a considerable population shift towards the open state as well as more pronounced conformational dynamics. Moreover, we capture four conformational states of the S-trimer/ACE2 complex for each of the two variants, revealing an enlarged conformational landscape for the Kappa and Beta S-ACE2 complexes and pronounced population shift towards the three RBDs up conformation. These results implicate that the mutations in Kappa and Beta may modify the kinetics of receptor binding and viral fusion to improve virus fitness. Combined with biochemical analysis, our structural study shows that the two variants are enabled to efficiently interact with ACE2 receptor despite their sensitive ACE2 binding surface is modified to escape recognition by some potent neutralizing MAbs. Our findings shed new light on the pathogenicity and immune evasion mechanism of the Beta and Kappa variants.
History
DepositionNov 12, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vxd
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_32176.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.)
1.09 Å/pix.
x 360 pix.
= 393.48 Å
1.09 Å/pix.
x 360 pix.
= 393.48 Å
1.09 Å/pix.
x 360 pix.
= 393.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density
Contour LevelBy AUTHOR: 0.703 / Movie #1: 0.8
Minimum - Maximum-1.5142765 - 3.0064306
Average (Standard dev.)0.0048002084 (±0.112914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 393.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0931.0931.093
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z393.480393.480393.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.5143.0060.005

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Supplemental data

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Sample components

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Entire SARS-CoV-2 spike protein in complex with ACE2, Beta Variant

EntireName: SARS-CoV-2 spike protein in complex with ACE2, Beta VariantCoronavirus spike protein
Number of Components: 5

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Component #1: protein, SARS-CoV-2 spike protein in complex with ACE2, Beta Variant

ProteinName: SARS-CoV-2 spike protein in complex with ACE2, Beta VariantCoronavirus spike protein
Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

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Component #2: protein, SARS-CoV-2 spike protein

ProteinName: SARS-CoV-2 spike proteinCoronavirus spike protein / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, ACE2

ProteinName: ACE2Angiotensin-converting enzyme 2 / Recombinant expression: No

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinSpike protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 139.650516 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Angiotensin-converting enzyme 2

ProteinName: Angiotensin-converting enzyme 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.396492 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
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: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 9689
3D reconstructionResolution: 4 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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