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- EMDB-35623: SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state) -

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Basic information

Entry
Database: EMDB / ID: EMD-35623
TitleSARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state)
Map data
Sample
  • Complex: SARS-COV-2 XBB.1 spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsspike glycoprotein / 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 / suppression by virus 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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: 2.51 Å
AuthorsAnraku Y / Kita S / Yajima H / Sasaki J / Sasaki-Tabata K / 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: Nat Commun / Year: 2023
Title: Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants.
Authors: Tomokazu Tamura / Jumpei Ito / Keiya Uriu / Jiri Zahradnik / Izumi Kida / Yuki Anraku / Hesham Nasser / Maya Shofa / Yoshitaka Oda / Spyros Lytras / Naganori Nao / Yukari Itakura / Sayaka ...Authors: Tomokazu Tamura / Jumpei Ito / Keiya Uriu / Jiri Zahradnik / Izumi Kida / Yuki Anraku / Hesham Nasser / Maya Shofa / Yoshitaka Oda / Spyros Lytras / Naganori Nao / Yukari Itakura / Sayaka Deguchi / Rigel Suzuki / Lei Wang / Mst Monira Begum / Shunsuke Kita / Hisano Yajima / Jiei Sasaki / Kaori Sasaki-Tabata / Ryo Shimizu / Masumi Tsuda / Yusuke Kosugi / Shigeru Fujita / Lin Pan / Daniel Sauter / Kumiko Yoshimatsu / Saori Suzuki / Hiroyuki Asakura / Mami Nagashima / Kenji Sadamasu / Kazuhisa Yoshimura / Yuki Yamamoto / Tetsuharu Nagamoto / Gideon Schreiber / Katsumi Maenaka / / Takao Hashiguchi / Terumasa Ikeda / Takasuke Fukuhara / Akatsuki Saito / Shinya Tanaka / Keita Matsuno / Kazuo Takayama / Kei Sato /
Abstract: In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the ...In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.
History
DepositionMar 13, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35623.png

Downloads & links

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Map

FileDownload / File: emd_35623.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.098
Minimum - Maximum-0.35902545 - 0.8067933
Average (Standard dev.)0.0000155326 (±0.014915957)
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_35623_msk_1.map
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Additional map: #1

Fileemd_35623_additional_1.map
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Half map: #1

Fileemd_35623_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_35623_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-COV-2 XBB.1 spike glycoprotein

EntireName: SARS-COV-2 XBB.1 spike glycoprotein
Components
  • Complex: SARS-COV-2 XBB.1 spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-COV-2 XBB.1 spike glycoprotein

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

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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: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 138.076062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LLMGCVAETG SSQCVNLITR TQSYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPAL PFNDGVYFA STEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLDV YQKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String:
LLMGCVAETG SSQCVNLITR TQSYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPAL PFNDGVYFA STEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLDV YQKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKE GNFKNLREFV FKNIDGYFKI YSKHTPINLE RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LH RSYLTPV DSSSGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TES IVRFPN ITNLCPFHEV FNATTFASVY AWNRKRISNC VADYSVIYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IRGN EVSQI APGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKPSGNYN YLYRLFRKSK LKPFERDIST EIYQAGNKPC NGVAG SNCY SPLQSYGFRP TYGVGHQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQF GRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIHADQ LTPTWRVYST GSNVFQT RA GCLIGAEYVN NSYECDIPIG AGICASYQTQ TKSHGSAGSV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTE I LPVSMTKTSV DCTMYICGDS TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKY FGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPAL QIPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNH NAQALNTLVK Q LSSKFGAI SSVLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GK GYHLMSF PQSAPHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGN CDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGK YEQYI ASSGYIPEAP RDGQAYVRKD GEWVLLSTFL EGTKHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 36 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4 / Details: calcium- and magnesium-free PBS buffer.
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 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: 6312 / Average exposure time: 1.5 sec. / Average electron dose: 50.4 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: 1966806
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 160906
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8gs6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8iot:
Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state)

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