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- EMDB-14154: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14154
TitleSARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
Map dataSARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
Sample
  • Complex: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
    • Protein or peptide: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
KeywordsSARS-CoV-2 Spike / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsNaismith JH / Yang Y / Liu JW
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Science / Year: 2022
Title: Pathogen-sugar interactions revealed by universal saturation transfer analysis.
Authors: Charles J Buchanan / Ben Gaunt / Peter J Harrison / Yun Yang / Jiwei Liu / Aziz Khan / Andrew M Giltrap / Audrey Le Bas / Philip N Ward / Kapil Gupta / Maud Dumoux / Tiong Kit Tan / Lisa ...Authors: Charles J Buchanan / Ben Gaunt / Peter J Harrison / Yun Yang / Jiwei Liu / Aziz Khan / Andrew M Giltrap / Audrey Le Bas / Philip N Ward / Kapil Gupta / Maud Dumoux / Tiong Kit Tan / Lisa Schimaski / Sergio Daga / Nicola Picchiotti / Margherita Baldassarri / Elisa Benetti / Chiara Fallerini / Francesca Fava / Annarita Giliberti / Panagiotis I Koukos / Matthew J Davy / Abirami Lakshminarayanan / Xiaochao Xue / Georgios Papadakis / Lachlan P Deimel / Virgínia Casablancas-Antràs / Timothy D W Claridge / Alexandre M J J Bonvin / Quentin J Sattentau / Simone Furini / Marco Gori / Jiandong Huo / Raymond J Owens / Christiane Schaffitzel / Imre Berger / Alessandra Renieri / / James H Naismith / Andrew J Baldwin / Benjamin G Davis /
Abstract: Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or ...Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis.
History
DepositionJan 18, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14154.png

Downloads & links

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Map

FileDownload / File: emd_14154.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 376 pix.
= 308.32 Å		0.82 Å/pix.
x 376 pix.
= 308.32 Å		0.82 Å/pix.
x 376 pix.
= 308.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.671485 - 4.5147214
Average (Standard dev.)0.0062775123 (±0.116630055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 308.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 ...

EntireName: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
Components
  • Complex: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
    • Protein or peptide: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry

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Supramolecule #1: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 ...

SupramoleculeName: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 ...

MacromoleculeName: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPR RAASVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDKVE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQYIKWPSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 312018
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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