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- EMDB-60558: Sarbecovirus HeB2013 Spike Trimer in a Locked Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-60558
TitleSarbecovirus HeB2013 Spike Trimer in a Locked Conformation
Map data
Sample
  • Organelle or cellular component: HeB2013
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesBtRf-BetaCoV/HeB2013 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 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-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60558.png

Downloads & links

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Map

FileDownload / File: emd_60558.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.)
1.64 Å/pix.
x 256 pix.
= 420.48 Å		1.64 Å/pix.
x 256 pix.
= 420.48 Å		1.64 Å/pix.
x 256 pix.
= 420.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6425 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0185
Minimum - Maximum-0.10669229 - 0.17510991
Average (Standard dev.)0.00006225793 (±0.0036936821)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 420.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60558_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: #1

Fileemd_60558_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : HeB2013

EntireName: HeB2013
Components
  • Organelle or cellular component: HeB2013
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HeB2013

SupramoleculeName: HeB2013 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: the spike trimer
Source (natural)Organism: BtRf-BetaCoV/HeB2013 (virus)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: BtRf-BetaCoV/HeB2013 (virus)
Molecular weightTheoretical: 138.951797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKILIFAFLV TLVKAQEGCG VINLKTQPIL TQVSSSRRGV YYNDDIFRSD VLHLTQDYFL PFHSNLTQYF SLNIESDKIV YFDNPILKF GDGVYFAATE KSNVIRGWVF GSTFDNTTQS AIIVNNSTHI IIRVCYFNLC KDPMYTVSAG TQVSSWVYQS A FNCTYDRV ...String:
MKILIFAFLV TLVKAQEGCG VINLKTQPIL TQVSSSRRGV YYNDDIFRSD VLHLTQDYFL PFHSNLTQYF SLNIESDKIV YFDNPILKF GDGVYFAATE KSNVIRGWVF GSTFDNTTQS AIIVNNSTHI IIRVCYFNLC KDPMYTVSAG TQVSSWVYQS A FNCTYDRV EKSFQLDTSP KTGNFTDLRE FVFKNRDGFF TVYQTYTPVN LLRGLPSGLS VLKPILKLPF GINITSFRVV MA MFSKTTS NYVPESAAYY VGNLKQSTFM LSFNQNGTIV DAVDCSQDPL AELKCTTKSF NVSKGIYQTS NFRVSPVTEV VRF PNITNL CPFDKVFNAT RFPSVYAWER TKISDCVADY TVFYNSTSFS TFNCYGVSPS KLIDLCFTSV YADTFLIRFS EVRQ VAPGQ TGVIADYNYK LPDDFTGCVI AWNTAKQDVG SYFYRSHRSS KLKPFERDLS SEENGVRTLS TYDFNQYVPL EYQAT RVVV LSFELLNAPA TVCGPKLSTS LVKNQCVNFN FNGFKGTGVL TDSSKTFQSF QQFGRDASDF TDSVRDPQTL RILDIS PCS FGGVSVITPG TNTSSAVAVL YQDVNCTDVP TTLHADQLAP SWRVYTTGPY VFQTQAGCLI GAEHVNASYQ CDIPIGA GI CASYHTASLL RSTGQKSIVA YTMSLGAENS VAYANNSIAI PTNFSISVTT EVMPVSMAKT SVDCTMYICG DSLECSNL L LQYGSFCTQL NRALSGIAVE QDKNTQEVFA QVKQMYKTPT IRDFGGFNFS QILPDPLKPT KRSFIEDLLY NKVTLADAG FMKQYADCLG GINARDLICA QKFNGLTVLP PLLTDDMIAA YTAALISGTA TAGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQK QIANQFNKAI TQIQESLTTT STALGKLQDV VNQNAQALNT LVKQLSSNFG AISSALNDIL SRLDKVEAEV Q IDRLITGR LQSLQTYVTQ QLIRAAEIRT SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPS QE RNFTTAP AICHEGKAYF PREGVFVSNG SFWFITQRNF YSPQIITTDN TFVAGSCDVV IGIINNTVYD PLQPELDSFK QEL DKYFKN HTSPDVDLGD ISGINASVVD IQKEIDRLNE VAKNLNESLI DLQELGKYEQ GSGYIPEAPR DGQAYVRKDG EWVL LSTFL LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEKSA

UniProtKB: Spike glycoprotein

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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125937
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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