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- EMDB-65718: sarbecovirus Rc-o319 S-trimer in a locked-2 conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-65718
Titlesarbecovirus Rc-o319 S-trimer in a locked-2 conformation
Map data
Sample
  • Organelle or cellular component: the spike protein of Rc-o319
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA
Keywordsspike protein / VIRUS / VIRAL PROTEIN
Biological speciesSarbecovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang J / Li ZX / Li ZM / Huang Y / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82341085 China
CitationJournal: To Be Published
Title: sarbecovirus Rc-o319 S-trimer in a locked-2 conformation
Authors: Wang J / Li Z / Li ZM / Yuan H / Xiong X
History
DepositionAug 5, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65718.png

Downloads & links

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Map

FileDownload / File: emd_65718.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.051
Minimum - Maximum-0.12681468 - 0.30873454
Average (Standard dev.)0.0003078953 (±0.009754836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65718_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65718_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 : the spike protein of Rc-o319

EntireName: the spike protein of Rc-o319
Components
  • Organelle or cellular component: the spike protein of Rc-o319
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA

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Supramolecule #1: the spike protein of Rc-o319

SupramoleculeName: the spike protein of Rc-o319 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarbecovirus / Strain: Rc-o319

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus / Strain: Rc-o319
Molecular weightTheoretical: 138.931375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFILVLLNVL SVYGCVNITY GSHHLYVSSR TRGVYYPDDA FRSSTNVLHE GFFLPFDSNV TWYSFWNQKY SVATSPFGDG VYFSTIDKS NVVRGWVFGT TLDNDTQSVL LYNDGTHVRV EVCTFHFCPT PVFSASSPHL YSSAFNCTLN YTLASVRADF T EVDGSFKT ...String:
MFILVLLNVL SVYGCVNITY GSHHLYVSSR TRGVYYPDDA FRSSTNVLHE GFFLPFDSNV TWYSFWNQKY SVATSPFGDG VYFSTIDKS NVVRGWVFGT TLDNDTQSVL LYNDGTHVRV EVCTFHFCPT PVFSASSPHL YSSAFNCTLN YTLASVRADF T EVDGSFKT IREFVFKLQD GSLNVYYAST SYVLAIGATS QLPSGVTPLV PLWKIPIGLN ITNFKTLVYL RSDNTPLQAA YV VGHLKRR TMMFKYDENG TIVDAIDCAL DPLSETKCTL RSFIVEKGIY QTSNFRVQPQ DTVVRFPNIT NLCPFSEVFN ATT FASVYA WNRKRISNCV ADYSVLYNST SFSTFQCYGV SSTKLNDLCF TNVYADSFVV RGDEVRQIAP GQTGVIADYN YKLP DDFTG CVLAWNSRNQ DASTSGNFNY YYRIWRSEKL RPFERDIAHY DYQVGTQFKS SLKNYGFYSS AGDSHQPYRV VVLSF ELLN APATVCGPKQ STELIKNKCV NFNFNGLTGT GVLTDSNKKF QSFQQFGRDV SDFTDSVKDP KTLEVLDITP CSYGGV SVI TPGTNASTQV AVLYQDVNCT DVPTAIHAEQ LTPSWRVYST GTNMFQTQAG CLIGAEHVNN SYDCDIPIGA GICATYH TP SMLRSANNNK RIVAYVMSLG AENSVAYSNN TIAIPTNFTI SVTTEVMPVS MTKTSVDCTM YICGDSVECS TLLLQYGS F CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPDIKDFGG FNFSQILPDP SKPSKRSFIE DLLFNKVTLA DAGFVKQYG DCLGDIQARD LICAQKFNGL TVLPPLLTDE MIAAYTAALI SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKLIANQF NSAIGKIQES LTSTASALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDIISRLDKV EAEVQIDRLI T GRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQAA PHGVVFLHVT YIPSQERNFT TA PAICHEG KAHFPREGVF VSNGTHWFIT QRNFYEPQII TTDNTFVSGT CDVVIGIVNN TVYDPLQPEL ESFKDELDKY FKN HTSPDI DLGDISGINA SVVDIQKEID ILKDVAKNLN ESLINLQELG KYEQYIKWPG SGYIPEAPRD GQAYVRKDGE WVLL STFLL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSAW SHPQFEKSA

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 42 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 5 / Number of copies: 3 / Formula: BLA
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

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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: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xu2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86709
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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