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- EMDB-34223: SARS-CoV-2 BA.2.75 spike glycoprotein (1-up state) -

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Basic information

Entry
Database: EMDB / ID: EMD-34223
TitleSARS-CoV-2 BA.2.75 spike glycoprotein (1-up state)
Map data0.0802
Sample
  • Complex: SARS-COV-2 BA.2.75 spike glycoprotein
    • Protein or peptide: SARS-CoV-2 BA.2.75 spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsAnraku Y / Tabata-Sasaki K / Kita S / Fukuhara H / Maenaka K / Hashiguchi T
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101093 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Science and TechnologyJPMJCR20H8 Japan
Japan Society for the Promotion of Science (JSPS)JPJSCCA20190008 Japan
Japan Society for the Promotion of Science (JSPS)20H05773 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05873 Japan
CitationJournal: Cell Host Microbe / Year: 2022
Title: Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant.
Authors: Akatsuki Saito / Tomokazu Tamura / Jiri Zahradnik / Sayaka Deguchi / Koshiro Tabata / Yuki Anraku / Izumi Kimura / Jumpei Ito / Daichi Yamasoba / Hesham Nasser / Mako Toyoda / Kayoko Nagata ...Authors: Akatsuki Saito / Tomokazu Tamura / Jiri Zahradnik / Sayaka Deguchi / Koshiro Tabata / Yuki Anraku / Izumi Kimura / Jumpei Ito / Daichi Yamasoba / Hesham Nasser / Mako Toyoda / Kayoko Nagata / Keiya Uriu / Yusuke Kosugi / Shigeru Fujita / Maya Shofa / Mst Monira Begum / Ryo Shimizu / Yoshitaka Oda / Rigel Suzuki / Hayato Ito / Naganori Nao / Lei Wang / Masumi Tsuda / Kumiko Yoshimatsu / Jin Kuramochi / Shunsuke Kita / Kaori Sasaki-Tabata / Hideo Fukuhara / Katsumi Maenaka / Yuki Yamamoto / Tetsuharu Nagamoto / Hiroyuki Asakura / Mami Nagashima / Kenji Sadamasu / Kazuhisa Yoshimura / Takamasa Ueno / Gideon Schreiber / Akifumi Takaori-Kondo / / Kotaro Shirakawa / Hirofumi Sawa / Takashi Irie / Takao Hashiguchi / Kazuo Takayama / Keita Matsuno / Shinya Tanaka / Terumasa Ikeda / Takasuke Fukuhara / Kei Sato /
Abstract: The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2. ...The SARS-CoV-2 Omicron BA.2.75 variant emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically distinct from BA.5, the currently predominant BA.2 descendant. Here, we show that BA.2.75 has a greater effective reproduction number and different immunogenicity profile than BA.5. We determined the sensitivity of BA.2.75 to vaccinee and convalescent sera as well as a panel of clinically available antiviral drugs and antibodies. Antiviral drugs largely retained potency, but antibody sensitivity varied depending on several key BA.2.75-specific substitutions. The BA.2.75 spike exhibited a profoundly higher affinity for its human receptor, ACE2. Additionally, the fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were greater than those of BA.2. Our multilevel investigations suggest that BA.2.75 acquired virological properties independent of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.
History
DepositionSep 5, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34223.png

Downloads & links

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Map

FileDownload / File: emd_34223.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation0.0802
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 384 pix.
= 385.92 Å		1.01 Å/pix.
x 384 pix.
= 385.92 Å		1.01 Å/pix.
x 384 pix.
= 385.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0802
Minimum - Maximum-0.28826565 - 0.7149614
Average (Standard dev.)-4.522405e-05 (±0.016669521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 385.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34223_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 0.227

Fileemd_34223_half_map_1.map
Annotation0.227
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 0.227

Fileemd_34223_half_map_2.map
Annotation0.227
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-COV-2 BA.2.75 spike glycoprotein

EntireName: SARS-COV-2 BA.2.75 spike glycoprotein
Components
  • Complex: SARS-COV-2 BA.2.75 spike glycoprotein
    • Protein or peptide: SARS-CoV-2 BA.2.75 spike glycoprotein

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Supramolecule #1: SARS-COV-2 BA.2.75 spike glycoprotein

SupramoleculeName: SARS-COV-2 BA.2.75 spike glycoprotein / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: SARS-CoV-2 BA.2.75 spike glycoprotein

MacromoleculeName: SARS-CoV-2 BA.2.75 spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LLMGCVAETG SSQCVNLITR TQSYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHENNKSRME SELRVYSSAN NCTFEYVSQP ...String:
LLMGCVAETG SSQCVNLITR TQSYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHENNKSRME SELRVYSSAN NCTFEYVSQP FLMDLEGKQG NFKNLREFVF KNIDGYFKIY SKHTPVNLGR DLPQGFSALE PLVDLPIGIN ITRFQTLLAL HRSYLTPGDS SSSWTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNITN LCPFHEVFNA TRFASVYAWN RKRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIRG NEVSQIAPGQ TGNIADYNYK LPDDFTGCVI AWNSNKLDSK VSGNYNYLYR LFRKSKLKPF ERDISTEIYQ AGNKPCNGVA GFNCYFPLQS YGFRPTYGVG HQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFLPFQQ FGRDIADTTD AVRDPQTLEI LDITPCSFGG VSVITPGTNT SNQVAVLYQG VNCTEVPVAI HADQLTPTWR VYSTGSNVFQ TRAGCLIGAE YVNNSYECDI PIGAGICASY QTQTKSHGSA GSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFSQ ILSDPSKPSK RSPIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FKGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGPAL QIPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNH NAQALNTLVK QLSSKFGAIS SVLNDIFSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KGYHLMSFPQ SAPHGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITTDNTFVSG NCDVVIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQYIASSG YIPEAPRDGQ AYVRKDGEWV LLSTFLEGTK HHHHHH

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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

Concentration1.2 mg/mL
BufferpH: 7.4
Details: Octyl glucoside solution was added to PBS solution to a final concentration of 0.01%
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blotting time 5 s and blotting force 5..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 3308 / Average exposure time: 1.5 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 754589
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 96181
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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