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- EMDB-38459: Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state) -

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Basic information

Entry
Database: EMDB / ID: EMD-38459
TitleStructure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
Map data
Sample
  • Complex: SARS-CoV-2 BA.2.86 spike glycoprotein
    • Other: Spike glycoprotein
Keywordsspike protein / glycoprotein / VIRUS / 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: 3.32 Å
AuthorsYajima H / Anraku Y / Kita S / Kimura 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: 2024
Title: Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Authors: Hisano Yajima / Yuki Anraku / Yu Kaku / Kanako Terakado Kimura / Arnon Plianchaisuk / Kaho Okumura / Yoshiko Nakada-Nakura / Yusuke Atarashi / Takuya Hemmi / Daisuke Kuroda / Yoshimasa ...Authors: Hisano Yajima / Yuki Anraku / Yu Kaku / Kanako Terakado Kimura / Arnon Plianchaisuk / Kaho Okumura / Yoshiko Nakada-Nakura / Yusuke Atarashi / Takuya Hemmi / Daisuke Kuroda / Yoshimasa Takahashi / Shunsuke Kita / Jiei Sasaki / Hiromi Sumita / / Jumpei Ito / Katsumi Maenaka / Kei Sato / Takao Hashiguchi /
Abstract: Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its ...Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to facilitate the conformational shift to RBD-up remains unclear. Herein, we present the structures of the BA.2.86 and the JN.1 spike proteins bound to ACE2. Notably, we successfully observed the ACE2-bound down-RBD, indicating an intermediate structure before the RBD-up conformation. The wider and mobile angle of RBDs in the up-state provides space for ACE2 to interact with the down-RBD, facilitating the transition to the RBD-up state. The K356T, but not N354-linked glycan, contributes to both of infectivity and neutralizing-antibody evasion in BA.2.86. These structural insights the spike-protein dynamics would help understand the mechanisms underlying SARS-CoV-2 infection and its neutralization.
History
DepositionDec 26, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38459.png

Downloads & links

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Map

FileDownload / File: emd_38459.map.gz / Format: CCP4 / Size: 216 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.)
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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0802
Minimum - Maximum-0.30962282 - 0.72483563
Average (Standard dev.)-0.00043416463 (±0.017367065)
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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Additional map: #1

Fileemd_38459_additional_1.map
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Half map: #1

Fileemd_38459_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_38459_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV-2 BA.2.86 spike glycoprotein

EntireName: SARS-CoV-2 BA.2.86 spike glycoprotein
Components
  • Complex: SARS-CoV-2 BA.2.86 spike glycoprotein
    • Other: Spike glycoprotein

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Supramolecule #1: SARS-CoV-2 BA.2.86 spike glycoprotein

SupramoleculeName: SARS-CoV-2 BA.2.86 spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: other / ID: 1 / Classification: other
SequenceString: SSQCVMPLFN LITTTQSYTN SFTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVFIKVCE FQFCNDPFLD VYHKNNKSWM ESESGVYSSA NNCTFEYVSQ PFLMDLEGKQ ...String:
SSQCVMPLFN LITTTQSYTN SFTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVFIKVCE FQFCNDPFLD VYHKNNKSWM ESESGVYSSA NNCTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPIIGR DFPQGFSALE PLVDLPIGIN ITRFQTLLAL NRSYLTPGDS SSGWTAGAAD YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNVTN LCPFHEVFNA TRFASVYAWN RTRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIKG NEVSQIAPGQ TGNIADYNYK LPDDFTGCVI AWNSNKLDSK HSGNYDYWYR LFRKSKLKPF ERDISTEIYQ AGNKPCKGKG PNCYFPLQSY GFRPTYGVGH QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLTKS NKKFLPFQQF GRDIVDTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVSVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSRGSAG SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLFSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQLEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQYIASSGY IPEAPRDGQA YVRKDGEWVL LSTFLEGTKH HHHHH

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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
Component:
ConcentrationFormulaName
0.14 mol/LNaClsodium chloride
0.0027 mol/LKClkalium chloride
0.01 mol/LH3PO4phosphoric acid
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 3500 / 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 / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 32669
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8iou


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

PDB-8xux:
Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)

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