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- EMDB-16441: Omicron B.1.1.529 2 RBD up conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-16441
TitleOmicron B.1.1.529 2 RBD up conformation
Map data
Sample
  • Complex: Omicron Spike trimeric complex
    • Protein or peptide: Spike glycoprotein
KeywordsCOVID-19 / SPIKE TRIMER / OMICRON / B.1.1.529 / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...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 N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / 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
Biological speciesAlphacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRaghavan SSR / Walker MR / Salanti A / Barfod LK / Wang KT
Funding support Denmark, 3 items
OrganizationGrant numberCountry
Danish Council for Independent Research118248 Denmark
The Carlsberg FoundationCF20-0045 Denmark
Novo Nordisk FoundationNNF170C0026778 Denmark
CitationJournal: To Be Published
Title: Omicron B.1.1.529 2 RBD up conformation
Authors: Raghavan SSR / Walker MR / Salanti A / Barfod LK / Wang KT
History
DepositionJan 10, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16441.png

Downloads & links

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Map

FileDownload / File: emd_16441.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.5335692 - 2.4932928
Average (Standard dev.)-0.00043143303 (±0.05245601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 399.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16441_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16441_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16441_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Omicron Spike trimeric complex

EntireName: Omicron Spike trimeric complex
Components
  • Complex: Omicron Spike trimeric complex
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Omicron Spike trimeric complex

SupramoleculeName: Omicron Spike trimeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Alphacoronavirus
Molecular weightTheoretical: 0.4 kDa/nm

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Alphacoronavirus
Molecular weightTheoretical: 118.193594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LDVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE G KQGNFKNL ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LDVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE G KQGNFKNL REFVFKNIDG YFKIYSKHTP IIVPEDLPQG FSALEPLVDL PIGINITRFQ TLLALHRSSS GWTAGAAAYY VG YLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFDEVFNAT RFA SVYAWN RKRISNCVAD YSVLYNLAPF FTFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGNIADYNYK LPDD FTGCV IAWNSKNLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGFNCYFPLR SYSFRPTYGV GHQPY RVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLKGTGVL TESNKKFLPF QQFGRDIADT TDAVRDPQTL EILDIT PCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVN VFQTRAGCLI GAEYVNNSYE CDIPIGAGIC ASYQTSQSII AYTMSLG AE NSVAYSNNSI AIPTNFTISV TTEILPVSMT KTSVDCTMYI CGDSTECSNL LLQYGSFCTQ LKRALTGIAV EQDKNTQE V FAQVKQIYKT PPIKYFGGFN FSQILPDPSK SKRSFIEDLL FNKVTKFKGL TVLPPLLTDE MIAQYTSALL AGTITSGWT FGAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNHNAQ ALNTLVKQLS SKFGAISSV LNDIFSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG Y HLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CD VVIGIVN NTVYDPLQPE LDS

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

Concentration0.1 mg/mL
BufferpH: 7.5
GridModel: Homemade / Material: GRAPHENE OXIDE / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dk6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19500
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8c5r:
Omicron B.1.1.529 2 RBD up conformation

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