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- EMDB-60556: Sarbecovirus RmYN02 Spike Trimer in a Locked Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-60556
TitleSarbecovirus RmYN02 Spike Trimer in a Locked Conformation
Map data
Sample
  • Organelle or cellular component: the spike protein of RmYN02
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsspike protein / VIRAL PROTEIN
Biological speciesSarbecovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang J / Xiong X
Funding support2 items
OrganizationGrant numberCountry
Other government2022A1515110495
Other governmentSRPG22-002
CitationJournal: Sci Adv / Year: 2025
Title: SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding.
Authors: Jingjing Wang / Yong Ma / Zimu Li / Hang Yuan / Banghui Liu / Zexuan Li / Mengzhen Su / Gul Habib / Yutong Liu / Lutang Fu / Peiyi Wang / Mei Li / Jun He / Jing Chen / Peng Zhou / Zhengli ...Authors: Jingjing Wang / Yong Ma / Zimu Li / Hang Yuan / Banghui Liu / Zexuan Li / Mengzhen Su / Gul Habib / Yutong Liu / Lutang Fu / Peiyi Wang / Mei Li / Jun He / Jing Chen / Peng Zhou / Zhengli Shi / Xinwen Chen / Xiaoli Xiong /
Abstract: High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)-related coronaviruses (SARSr-CoVs) remains ...High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)-related coronaviruses (SARSr-CoVs) remains incompletely understood. We report cryo-electron microscopy structures of eight different S-proteins from SARSr-CoVs found across Asia, Europe, and Africa. These S-proteins all adopt tightly packed, locked, prefusion conformations. These structures enable the classification of SARSr-CoV S-proteins into three types, based on their receptor-binding motif (RBM) structures and ACE2 binding characteristics. Type-2 S-proteins often preferentially bind bat ACE2 (bACE2) over hACE2. We report a structure of a type-2 BtKY72-RBD in complex with bACE2 to understand ACE2 specificity. Structure-guided mutagenesis of BtKY72-RBD reveals that multiple synergistic mutations in four different regions of RBM are required to achieve high-affinity hACE2 binding. Similar RBM changes can also confer hACE2 binding to another type-2 BM48-31 S-protein, which is primarily non-ACE2 binding. These results provide an understanding of how high-affinity hACE2 binding may be acquired by SARSr-CoV S-proteins.
History
DepositionJun 16, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60556.png

Downloads & links

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Map

FileDownload / File: emd_60556.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.082045615 - 0.14840056
Average (Standard dev.)0.00010062288 (±0.005479357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60556_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60556_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 RmYN02

EntireName: the spike protein of RmYN02
Components
  • Organelle or cellular component: the spike protein of RmYN02
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: the spike protein of RmYN02

SupramoleculeName: the spike protein of RmYN02 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarbecovirus

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: RmYN02 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus
Molecular weightTheoretical: 136.450047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFILLLIGYT AATTCVTGPT IENKQNVSSL MRGVYYPDDI YRSNVNVLFT VPFLRFNSTL TWYNFWNQAY TSRVMEFGDG IYFSTVDKS NAVRGWIFGT TLDNTTQSAL LINNGSLVTI QVCYFQFCAN PAFLVAGGQQ TSAAVYISSH NCTYSEVLSH I SLDFTEDT ...String:
MFILLLIGYT AATTCVTGPT IENKQNVSSL MRGVYYPDDI YRSNVNVLFT VPFLRFNSTL TWYNFWNQAY TSRVMEFGDG IYFSTVDKS NAVRGWIFGT TLDNTTQSAL LINNGSLVTI QVCYFQFCAN PAFLVAGGQQ TSAAVYISSH NCTYSEVLSH I SLDFTEDT GSFKRLREFV FKNNDGFLHI YGAYQPHVID IGATPSLPST FKPLIPLWKL PLGLNITNFK VVLTFRSNSQ PL QANFAVG SLKLTTIMLS FDVNGTIDKA VDCSSDPLSE LKCTLKSFNV SKGIYPTSNF RILPSTEVVR FPNITNFCPF DKV FNATRF PNVYAWQRTK ISDCIADYTV LYNSTSFSTF KCYGVSPSKL IDLCFTSVYA DTFLIRFSEV RQIAPGETGV IADY NYKLP DDFTGCVLAW NTAQQDIGSY FYRSHRAVKL KPFERDLSSD ENGVRTLSTY DFNPNVPLDY QATRVVVLSF ELLNA PATV CGPKLSTQLV KNRCVNFNFN GLRGTGVLTD SDKRFQSFQQ FGRDSADFTD SVRDPQTLQI LDISPCSFGG VSVITP GTQ TSSKVAVLYQ DVNCTDVPTA LGLDQISAAW RVYAIGNDVF QTQAGCLVGA EHTNISYECD IPIGAGVCAS YNSPAAR VG TNSIIAYAMS IGAESSIAYS NNSIAIPTNF SIQVTTEVLP VSVSKTSVDC TMYICGDSQE CNKLLLQYGS FCAQLNRA L SGVAVEQDKN TEAVFAQVKQ IYKAPVIKDL GGFNFSQLLP DPTKPSQRSF IEDLLFDKVT LSDAGFIKQY GDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAAYTSA LVSGTATAGW TFGIGAALQV PFAMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALNTLVKQ LSSNFGAISS VLNDILSRLD KVEAEVQIDR LITGRLQSLQ T YVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KGYHLMSFPQ SAPHGVVFLH VTYVPAQEKN FTTAPAICYD GK AHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GSCDVVIGIV NNTVYDPLQP ELDSFKEELD KYFKNHTSPD VDL GDISGI NASVVNIQKE IDRLNEVAKN LNESLIDLQE LGKYEQGSGY IPEAPRDGQA YVRKDGEWVL LSTFLLEVLF QGPG HHHHH HHHSAWSHPQ FEKGGGSGGG GSGGSAWSHP QFEKSA

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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: 45 / 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
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4disodium hydrogen phosphate
1.8 mMKH2PO4potassium dihydrogen phosphate

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: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 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:

6pz2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27757
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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