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- EMDB-60551: Sarbecovirus BtKY72 Spike Trimer in a Locked Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-60551
TitleSarbecovirus BtKY72 Spike Trimer in a Locked Conformation
Map data
Sample
  • Organelle or cellular component: BtKY72/Rhinolophus sp./Kenya/2007
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA
Keywordsspike protein / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Betacoronavirus spike glycoprotein S1, receptor binding ...Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 speciesBtKY72 (virus) / Kenya bat coronavirus BtKY72
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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_60551.png

Downloads & links

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Map

FileDownload / File: emd_60551.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.)
1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.15582582 - 0.26736516
Average (Standard dev.)0.0003841593 (±0.008177583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60551_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_60551_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 : BtKY72/Rhinolophus sp./Kenya/2007

EntireName: BtKY72/Rhinolophus sp./Kenya/2007
Components
  • Organelle or cellular component: BtKY72/Rhinolophus sp./Kenya/2007
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA

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Supramolecule #1: BtKY72/Rhinolophus sp./Kenya/2007

SupramoleculeName: BtKY72/Rhinolophus sp./Kenya/2007 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: the spike trimer
Source (natural)Organism: BtKY72 (virus)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: delete residues 1194-1257.Sequence reference for source organism Kenya bat coronavirus BtKY72 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3Q8AKM0.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Kenya bat coronavirus BtKY72
Molecular weightTheoretical: 132.339625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFFILLSLL SFTTAQEGCG ILSNKSNPAL TQYFSSRRGF YYFDDTFRSS VRVLTTGYFL PFNSNLTGYS SRNSVTGRLI QFDNPNIPF KDGLYFAATE RSNVIRGWIF GSTLDNTTQS AVLFNNGTHI VINVCNFYFC QDPMLAVANG SHFKSWVFLN A TNCTYNRV ...String:
MKFFILLSLL SFTTAQEGCG ILSNKSNPAL TQYFSSRRGF YYFDDTFRSS VRVLTTGYFL PFNSNLTGYS SRNSVTGRLI QFDNPNIPF KDGLYFAATE RSNVIRGWIF GSTLDNTTQS AVLFNNGTHI VINVCNFYFC QDPMLAVANG SHFKSWVFLN A TNCTYNRV HGFEIDPSPN TGSFIHLREH VFRNVDGFLY VYHNYERVDV YDNFPQGFSV LKPIFKLPFG LNITQFKVIM TL FSPTTSS FNADASVYFV GHLKPLTMLA EFDENGTITD AVDCSQDPLS ELKCTTKSLT VEKGIYQTSN FRVSPSTEVV RFP NITNLC PFGQVFNASN FPSVYAWERL RISDCVADYA VLYNSSSSFS TFKCYGVSPT KLNDLCFSSV YADYFVVKGD DVRQ IAPAQ TGVIADYNYK LPDDFTGCVL AWNTNSVDSK SGNNFYYRLF RHGKIKPYER DISNVLYNSA GGTCSSISQL GCYEP LKSY GFTPTVGVGY QPYRVVVLSF ELLNAPATVC GPKKSTELVK NKCVNFNFNG LTGTGVLTSS TKKFQPFQQF GRDVSD FTD SVRDPKTFEI LDISPCSYGG VSVITPGTNT SKAVAVLYQD VNCTDVPTMI HVEQVSSDWR VYAFNSYGNM FQTQAGC LV GAIYENTTYE CDIPIGAGIC AKFGSDKIRM GQESIVAYTM SIGEDQSIAY SNNIIAIPTN FSISVTTEVL PVSMTKTS V DCNMYICGDS TECSNLLLQY GSFCTQLNRA LSGIAVEQDR NTRDVFAQTK SIYKTPNIKD FGGFNFSQIL PDPKKLSYR SFIEDLLYNK VTLSDPGFMK QYGDCLGGIN ARDLICAQKF NGLTVLPPLL TDDMIAAYTA ALISGTATAG YTFGAGAALQ IPFAMQMAY RFNGIGVTQN VLYENQKQIA NQFNNAISKI QDSLTTTSAA LGKLQDVINQ NAVALNTLVK QLSSNFGAIS S VLNDILSR LDKVEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QA APHGVVF LHVTYVPSQQ QNFTTAPAIC HNGKAYFPRE GVFVMNGTHW FITQRNFYSP QVITTDNTFE SGSCDVVIGI INN TVYDPL QPELESFKQE LDKYFKNHTS PDVDFGDISG INASVVDIKK EIAHLNEIAK NLNESLIDLQ ELGKYEQ

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 51 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 6 / 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
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 TITAN
Image recordingFilm or detector model: GATAN K3 (6k 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

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Image processing

CTF correctionSoftware - Name: RELION (ver. 4.01) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6zp2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98797
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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