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- EMDB-34975: SARS-CoV-2 Delta variant spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-34975
TitleSARS-CoV-2 Delta variant spike protein
Map data
Sample
  • Complex: SARS-CoV-2 Delta variant spike protein
    • Protein or peptide: Spike glycoprotein
KeywordsSARS-CoV-2 / Delta / Spike protein / VIRAL PROTEIN
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsXu J / Cheng H / Liu N / Wang HW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Self-assembled superstructure alleviates air-water interface effect in cryo-EM.
Authors: Liming Zheng / Jie Xu / Weihua Wang / Xiaoyin Gao / Chao Zhao / Weijun Guo / Luzhao Sun / Hang Cheng / Fanhao Meng / Buhang Chen / Weiyu Sun / Xia Jia / Xiong Zhou / Kai Wu / Zhongfan Liu / ...Authors: Liming Zheng / Jie Xu / Weihua Wang / Xiaoyin Gao / Chao Zhao / Weijun Guo / Luzhao Sun / Hang Cheng / Fanhao Meng / Buhang Chen / Weiyu Sun / Xia Jia / Xiong Zhou / Kai Wu / Zhongfan Liu / Feng Ding / Nan Liu / Hong-Wei Wang / Hailin Peng /
Abstract: Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air- ...Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air-water interface during standard cryo-EM specimen preparation. The interaction of proteins with air-water interface will significantly impede the success of reconstruction and achievable resolution. Here, we highlight the critical role of impenetrable surfactant monolayers in passivating the air-water interface problems, and develop a robust effective method for high-resolution cryo-EM analysis, by using the superstructure GSAMs which comprises surfactant self-assembled monolayers (SAMs) and graphene membrane. The GSAMs works well in enriching the orientations and improving particle utilization ratio of multiple proteins, facilitating the 3.3-Å resolution reconstruction of a 100-kDa protein complex (ACE2-RBD), which shows strong preferential orientation using traditional specimen preparation protocol. Additionally, we demonstrate that GSAMs enables the successful determinations of small proteins (<100 kDa) at near-atomic resolution. This study expands the understanding of SAMs and provides a key to better control the interaction of protein with air-water interface.
History
DepositionDec 15, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34975.png

Downloads & links

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Map

FileDownload / File: emd_34975.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.977276 - 4.713538
Average (Standard dev.)-0.0014538004 (±0.081093304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34975_half_map_1.map
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34975_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV-2 Delta variant spike protein

EntireName: SARS-CoV-2 Delta variant spike protein
Components
  • Complex: SARS-CoV-2 Delta variant spike protein
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: SARS-CoV-2 Delta variant spike protein

SupramoleculeName: SARS-CoV-2 Delta variant spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: on graphene/SAMs membranes
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: For the issue of poor atom inclusion, the depositor stated 'we have tried our best to fit the coordinates in the density map of spike via rigid-body dock. However, the flexibility of RBD ...Details: For the issue of poor atom inclusion, the depositor stated 'we have tried our best to fit the coordinates in the density map of spike via rigid-body dock. However, the flexibility of RBD makes it hard to fit, which seems to be general for spike proteins.'
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 138.842375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPRGPVAALL LLILHGAWSC VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVISGTNGTK RFDNPVLPF NDGVYFASIE KSNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLDHKNN KSWMESEFRV Y SSANNCTF ...String:
MPRGPVAALL LLILHGAWSC VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVISGTNGTK RFDNPVLPF NDGVYFASIE KSNIIRGWIF GTTLDSKTQS LLIVNNATNV VIKVCEFQFC NDPFLDHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PIIVREPEDL PQGFSALEPL VDLPIGINIT RF QTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNF RVQPTE SIVRFPNITN LCPFDEVFNA TRFASVYAWN RKRISNCVAD YSVLYNLAPF FTFKCYGVSP TKLNDLCFTN VYAD SFVIR GDEVRQIAPG QTGNIADYNY KLPDDFTGCV IAWNSNKLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNK PCNG VAGFNCYFPL RSYSFRPTYG VGHQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLKGTGVL TESNKK FLP FQQFGRDIAD TTDAVRDPQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVP VAIHADQLTP TWRVYST GS NVFQTRAGCL IGAEYVNNSY ECDIPIGAGI CASYQTQTKS HGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNF T ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFG GFNFSQILPD PSKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFKGL TVLPPLLTDE MIAQYTSALL AGTITSGWT FGAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNHNAQ A LNTLVKQL SSKFGAISSV LNDIFSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SK RVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTD NTFVSG NCDVVIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLI DLQEL GKYEQLVPRG SGYIPEAPRD GQAYVRKDGE WVLLSTFLHH HHHH

UniProtKB: Spike glycoprotein

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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

Concentration0.25 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75650
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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