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- EMDB-62143: SARS-CoV-2 related bat coronavirus BANAL-52 spike in the locked state -

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Basic information

Entry
Database: EMDB / ID: EMD-62143
TitleSARS-CoV-2 related bat coronavirus BANAL-52 spike in the locked state
Map dataWe carefully examined the dataset and conducted an additional round of duplicate removal, eliminating 249 particles. However, after performing 3D refinement, no significant improvement in the FSC was observed. We then repeated the process using a looser mask, but the FSC still did not reach satisfactory levels. Subsequently, we re-extracted the selected particles using a smaller box size and carried out another round of 3D refinement. This time, we observed a slight improvement in the FSC, which now drops to zero, and still maintains a resolution of 3.5 angstrom.
Sample
  • Complex: SARS-CoV-2 related bat coronavirus BANAL-52 spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
KeywordsSARS-CoV-2 related bat coronavirus BANA-52 spike with linoleic acid binding / 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, receptor-binding domain, SARS-CoV-2 / 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, 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / 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, 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 speciesHorseshoe bat sarbecovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsLi QQ / Cai X / Li XN / Zhang YB / Li R / Kang ZR / Wan DD / Wang JX / Yang JX / Shi JX ...Li QQ / Cai X / Li XN / Zhang YB / Li R / Kang ZR / Wan DD / Wang JX / Yang JX / Shi JX / Jin SL / Peng Y / Zang N / Xie ZK / Wan YS / Shang J
Funding support China, 3 items
OrganizationGrant numberCountry
Other government32200113 China
Other government232301420013 China
Other government232102311001 China
CitationJournal: To Be Published
Title: Characteristics of Spike Activation,Structure and Host Proteases Adaption Revealed Limitations for SARS-CoV-2 related Coronavirus Cell Entry
Authors: Li QQ / Cai X / Li XN / Zhang YB / Li R / Kang ZR / Wan DD / Wang JX / Yang JX / Shi JX / Jin SL / Peng Y / Zang N / Xie ZK / Wan YS / Shang J
History
DepositionOct 22, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62143.png

Downloads & links

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Map

FileDownload / File: emd_62143.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWe carefully examined the dataset and conducted an additional round of duplicate removal, eliminating 249 particles. However, after performing 3D refinement, no significant improvement in the FSC was observed. We then repeated the process using a looser mask, but the FSC still did not reach satisfactory levels. Subsequently, we re-extracted the selected particles using a smaller box size and carried out another round of 3D refinement. This time, we observed a slight improvement in the FSC, which now drops to zero, and still maintains a resolution of 3.5 angstrom.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 256 pix.
= 424.96 Å		1.66 Å/pix.
x 256 pix.
= 424.96 Å		1.66 Å/pix.
x 256 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.07910304 - 0.17214268
Average (Standard dev.)0.00021715334 (±0.0034050564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62143_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62143_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_62143_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 : SARS-CoV-2 related bat coronavirus BANAL-52 spike protein

EntireName: SARS-CoV-2 related bat coronavirus BANAL-52 spike protein
Components
  • Complex: SARS-CoV-2 related bat coronavirus BANAL-52 spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID

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Supramolecule #1: SARS-CoV-2 related bat coronavirus BANAL-52 spike protein

SupramoleculeName: SARS-CoV-2 related bat coronavirus BANAL-52 spike protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Horseshoe bat sarbecovirus
Molecular weightTheoretical: 450 kDa/nm

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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: Horseshoe bat sarbecovirus
Molecular weightTheoretical: 138.414312 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SSTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAIHV SGTNGIKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHRNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SSTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAIHV SGTNGIKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHRNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPP GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCSLDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATT FASVYAWNRK RISNCVADYS VLYNSTSFST FKCYGVSPTK LNDLCFTNVY ADSF VVRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFHPTNGVG YQPYRVVVLS FELLNAPATV CGPKKSTNLI KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN ASNQVAVLYQ DVNCTEVPVA IHANQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSRS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTT E ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLNR ALTGIAVEQD KNTQEVFAQV KQIYKTPQIK DFGGFNFSQ ILPDPSKPSK RSFIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGAA LQIPFAMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLSSTAS ALGKLQDVVN QNAQALNTLV K QLSSNFGA ISSVLNDILS RLDPPEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CG KGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSG NCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLSDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELG KYEQY IKGSGSGYIP EAPRDGQAYV RKDGEWVLLS TFLGHHHHHH HH

UniProtKB: Spike glycoprotein

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 54 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #3: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 3 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20175
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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