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- EMDB-60552: Sarbecovirus BM48-31 Spike Trimer in a Locked Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-60552
TitleSarbecovirus BM48-31 Spike Trimer in a Locked Conformation
Map data
Sample
  • Organelle or cellular component: the spike protein of sarbecovirus BM48-31
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
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 (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 (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 speciesBM48-31 (virus) / Bat coronavirus BM48-31/BGR/2008
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_60552.png

Downloads & links

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Map

FileDownload / File: emd_60552.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 360 pix.
= 420.48 Å		1.17 Å/pix.
x 360 pix.
= 420.48 Å		1.17 Å/pix.
x 360 pix.
= 420.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.168 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.058181748 - 0.10242343
Average (Standard dev.)0.000025036667 (±0.0029974503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 420.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60552_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_60552_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 sarbecovirus BM48-31

EntireName: the spike protein of sarbecovirus BM48-31
Components
  • Organelle or cellular component: the spike protein of sarbecovirus BM48-31
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID

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Supramolecule #1: the spike protein of sarbecovirus BM48-31

SupramoleculeName: the spike protein of sarbecovirus BM48-31 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: the spike trimer
Source (natural)Organism: BM48-31 (virus)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: T4 trimerization foldon:GSGYIPEAPRDGQAYVRKDGEWVLLSTFL HRV 3C cleavage site:LEVLFQGP His-tag:HHHHHHHH strep tag:WSHPQFEKGGGSGGGGSGGSAWSHPQFEKSA
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bat coronavirus BM48-31/BGR/2008
Molecular weightTheoretical: 140.690406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFLAFLCLL GFANAQDGKC GTLSNKSPSK LTQTPSSRRG FYYFDDIFRS SIRVLTTGHF LPFNTNLTWY LTLKSNGKQR IYYDNPNIN FGDGVYFGLT EKSNVFRGWI FGSTLDNTTQ SAVLFNNGTH IVIDVCNFNF CADPMFAVNS GQPYKTWIYT S AANCTYHR ...String:
MKFLAFLCLL GFANAQDGKC GTLSNKSPSK LTQTPSSRRG FYYFDDIFRS SIRVLTTGHF LPFNTNLTWY LTLKSNGKQR IYYDNPNIN FGDGVYFGLT EKSNVFRGWI FGSTLDNTTQ SAVLFNNGTH IVIDVCNFNF CADPMFAVNS GQPYKTWIYT S AANCTYHR AHAFNISTNM NPGKFKHFRE HLFKNVDGFL YVYHNYEPID LNSGFPSGFS VLKPILKLPF GLNITYVKAI MT LFSSTQS NFDADASAYF VGHLKPLTML VDFDENGTII DAIDCSQDPL SELKCTTKSF TVEKGIYQTS NFRVTPTTEV VRF PNITQL CPFNEVFNIT SFPSVYAWER MRITNCVADY SVLYNSSASF STFQCYGVSP TKLNDLCFSS VYADYFVVKG DDVR QIAPA QTGVIADYNY KLPDDFTGCV IAWNTNSLDS SNEFFYRRFR HGKIKPYGRD LSNVLFNPSG GTCSAEGLNC YKPLA SYGF TQSSGIGFQP YRVVVLSFEL LNAPATVCGP KQSTELVKNK CVNFNFNGLT GTGVLTNSTK KFQPFQQFGR DVSDFT DSV RDPKTLEILD IAPCSYGGVS VITPGTNASS SVAVLYQDVN CTDVPTMLHA DQISHDWRVY AFRNDGNIFQ TQAGCLI GA AYDNSSYECD IPIGAGICAK YTNVSSTLVR SGGHSILAYT MSLGDNQDIV YSNNTIAIPM NFSISVTTEV LPVSMTKT S VDCNMYICGD STECSNLLLQ YGSFCTQLNR ALAGIAVEQD RNTRDVFAQT KAMYKTPSLK DFGGFNFSQI LPDPAKPSS RSFIEDLLYN KVTLADPGFM KQYGDCLGGV NARDLICAQK FNGLTVLPPL LTDEMIAAYT AALISGTATA GFTFGAGAAL QIPFAMQMA YRFNGIGVTQ NVLYENQKQI ANQFNKAISQ IQDSLSTTTT ALGKLQDVIN QNAIALNTLV KQLSSNFGAI S SVLNDILS RLDKVEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CGKGYHLMSF PQ AAPHGVV FLHVTYVPSQ EQNFTTAPAI CHEGKAHFPR EGVFVTNGTH WFITQRNFYS PQPITTDNTF VSGNCDVVIG IVN NTVYDP LQPELDSFKE ELDKYFKNHT SQNVSLDGLN NINASVVDIK KEIEHLNEIA KSLNESLIDL QELGKYEQGS GYIP EAPRD GQAYVRKDGE WVLLSTFLLE VLFQGPGHHH HHHHHSAWSH PQFEKGGGSG GGGSGGSAWS HPQFEKSA

UniProtKB: Spike glycoprotein

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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: 39 / 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: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79256
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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