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- EMDB-22932: Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at... -

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Entry
Database: EMDB / ID: EMD-22932
TitleCryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4
Map data
SampleCryo-EM structure of Double ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4:
Spike glycoproteinSpike protein / Angiotensin-converting enzyme 2 / ligand
Function / homology
Function and homology information


positive regulation of L-proline import across plasma membrane / positive regulation of amino acid transport / 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 / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity ...positive regulation of L-proline import across plasma membrane / positive regulation of amino acid transport / 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 / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity / regulation of vasoconstriction / blood vessel diameter maintenance / Attachment and Entry / angiotensin maturation / carboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / brush border membrane / metallocarboxypeptidase activity / regulation of cytokine production / negative regulation of signaling receptor activity / regulation of cardiac conduction / regulation of transmembrane transporter activity / cilium / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / metallopeptidase activity / regulation of cell population proliferation / endoplasmic reticulum-Golgi intermediate compartment / virus receptor activity / positive regulation of reactive oxygen species metabolic process / viral translation / Potential therapeutics for SARS / host cell surface receptor binding / regulation of inflammatory response / endocytosis involved in viral entry into host cell / 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 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
Renal amino acid transporter / Collectrin domain / Angiotensin-converting enzyme / Peptidase M2, peptidyl-dipeptidase A / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus ...Renal amino acid transporter / Collectrin domain / Angiotensin-converting enzyme / Peptidase M2, peptidyl-dipeptidase A / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / 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 / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Neutral zinc metallopeptidases, zinc-binding region signature.
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: 3.62 Å
AuthorsGorman J / Kwong PD / Shapiro L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Other privateSF349247 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Authors: Tongqing Zhou / Yaroslav Tsybovsky / Jason Gorman / Micah Rapp / Gabriele Cerutti / Gwo-Yu Chuang / Phinikoula S Katsamba / Jared M Sampson / Arne Schön / Jude Bimela / Jeffrey C Boyington ...Authors: Tongqing Zhou / Yaroslav Tsybovsky / Jason Gorman / Micah Rapp / Gabriele Cerutti / Gwo-Yu Chuang / Phinikoula S Katsamba / Jared M Sampson / Arne Schön / Jude Bimela / Jeffrey C Boyington / Alexandra Nazzari / Adam S Olia / Wei Shi / Mallika Sastry / Tyler Stephens / Jonathan Stuckey / I-Ting Teng / Pengfei Wang / Shuishu Wang / Baoshan Zhang / Richard A Friesner / David D Ho / John R Mascola / Lawrence Shapiro / Peter D Kwong /
Abstract: The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand ...The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
History
DepositionNov 3, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: RCSB / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.2
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
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  • Surface view with fitted model
  • Atomic models: PDB-7kmz
  • Surface level: 0.2
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_22932.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 444.36 Å
1.06 Å/pix.
x 420 pix.
= 444.36 Å
1.06 Å/pix.
x 420 pix.
= 444.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.2
Minimum - Maximum-0.45309198 - 1.17846
Average (Standard dev.)0.0007796757 (±0.03272281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 444.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z444.360444.360444.360
α/β/γ90.00090.00090.000
start NX/NY/NZ937643
NX/NY/NZ114126230
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.4531.1780.001

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Supplemental data

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Segmentation: #1

Fileemd_22932_msk_1.map
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Additional map: Additional Vol 1

Fileemd_22932_additional_1.map
AnnotationAdditional Vol 1
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Half map: half-volume 1

Fileemd_22932_half_map_1.map
Annotationhalf-volume 1
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Half map: half-volume 2

Fileemd_22932_half_map_2.map
Annotationhalf-volume 2
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Sample components

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Entire Cryo-EM structure of Double ACE2-bound SARS-CoV-2 Trimer Spike at...

EntireName: Cryo-EM structure of Double ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4
Number of Components: 4

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Component #1: protein, Cryo-EM structure of Double ACE2-bound SARS-CoV-2 Trimer...

ProteinName: Cryo-EM structure of Double ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4
Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoproteinSpike protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 142.399375 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
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: 69.153664 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 53 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 53.49 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 / Applied Symmetry: C1 (asymmetric) / Number of Projections: 48008
3D reconstructionAlgorithm: FOURIER SPACE / Software: cryoSPARC / Resolution: 3.62 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Input PDB model: 7KMS
Output model

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