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- EMDB-61152: Cryo-EM structure of Bat SARS-like coronavirus Khosta-2 spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-61152
TitleCryo-EM structure of Bat SARS-like coronavirus Khosta-2 spike protein
Map data
Sample
  • Complex: Spike protein of Bat SARS-like coronavirus Khosta-2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA
  • Ligand: LINOLEIC ACID
KeywordsKhosta-2 / spike protein / VIRAL PROTEIN / coronavirus
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, 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 (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 / 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, 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 speciesBat SARS-like coronavirus Khosta-2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsPan XQ / Li LJ / Liu KF / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural basis of receptor recognition by Khosta-1/Khosta-2 spike proteins
Authors: Pan XQ / Li LJ / Liu KF
History
DepositionAug 13, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61152.png

Downloads & links

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Map

FileDownload / File: emd_61152.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 520 pix.
= 457.6 Å		0.88 Å/pix.
x 520 pix.
= 457.6 Å		0.88 Å/pix.
x 520 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-0.5560897 - 1.5990728
Average (Standard dev.)-0.0007076155 (±0.030261364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61152_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61152_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_61152_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 : Spike protein of Bat SARS-like coronavirus Khosta-2

EntireName: Spike protein of Bat SARS-like coronavirus Khosta-2
Components
  • Complex: Spike protein of Bat SARS-like coronavirus Khosta-2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA
  • Ligand: LINOLEIC ACID

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Supramolecule #1: Spike protein of Bat SARS-like coronavirus Khosta-2

SupramoleculeName: Spike protein of Bat SARS-like coronavirus Khosta-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bat SARS-like coronavirus Khosta-2

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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: Bat SARS-like coronavirus Khosta-2
Molecular weightTheoretical: 136.230719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GAQDGCATLS TKLTPTQLQV NSTRRGFYYF DDIYRSSLRV LVPGYFLPFG TNITRYQAQV INWTAIFFDN PVIPFNDGVY FAALEHSNV VRGWIFGTTL DNTTQSAIVV NNATHILISV CYFNVCKEPM FAVSNFKPYK SWVYDRANNC TFNRAYPLNI S TTPEPGKF ...String:
GAQDGCATLS TKLTPTQLQV NSTRRGFYYF DDIYRSSLRV LVPGYFLPFG TNITRYQAQV INWTAIFFDN PVIPFNDGVY FAALEHSNV VRGWIFGTTL DNTTQSAIVV NNATHILISV CYFNVCKEPM FAVSNFKPYK SWVYDRANNC TFNRAYPLNI S TTPEPGKF KALREQVFRY QDGFLYIYHS YESINSDTLP PGFSVLKPML KLPLGLNITR FRVVMAMHSL TTSNFNTHSV NY FVGHLKP LTMLVEFSPN GTIIDAIDCS QDPLSELKCT TKSFSVEKGI YQTSNFRVSP SLDVVRFPNM TNICPFDQVF NKT QFPSVY AWERVRISDC VSDYTVLYNS SASFSTFKCY GVSPTKLNDL CFSGVYADYF VVKGDHVHQI APGQTGVIAD YNYK LPSEF VGCILAWNTR TIDSKRGFYY RLFRHGNIRP YERDTSNVPY NAAGGTCNQP GTHNCYEPLQ DYGFTSTSGV GYQPF RVVV LSFELLNAPA TVCGPKQSTD LVKNKCVNFN FNGLTGTGVL TDSNKKFQPF QQFGRDSADF TDSVKDPKTL EILDIT PCS YGGVSVITPG TNTSDSVAVL YQDVNCTDVP TMLHMDQVSN DWRVYAVNTD GNMFQTQAGC LVGATYDNTS YECDIPV GA GVCAKFQTTT RAKQSSILAY TMSLGEDSNV AYSNNSIAIP TNFTISVTTE VLPVSMTKTA VDCNMYICGD STECSSLL L QYGSFCQQLN RALAGVSVEQ DKNTQDVFAQ VKSIYKVSAI KDFGGFNFSQ ILPDPAKPSK RSPIEDLLYN KVTLADPGF MKQYGDCLGG VNARDLICAQ KFNGLTVLPP LLTDDMIAAY TSALVSGTAL SGFTFGAGPA LQIPFPMQMA YRFNGIGVTQ NVLYENQKQ IANQFNKAIS QIQESLTTTP TALGKLQDVI NQNAIALNTL VKQLSSNFGA ISSVLNDILS RLDPPEAEVQ I DRLITGRL QSLQTYVTQQ LIRAADIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FPQAAPHGVV FLHVTYVPSQ DK NFTTAPA ICHKGKAYFP REGVFVTNGT HWFVTQRNFY QPEVITTENT FESGNCDVVI GIVNNTVYDP LQPELESFKE ELD KYFKNH TSPDVDFDDI SGINASVVDI KKEIEHLNEI AKSLNESLID LQELGKYEQY IKWPWGGGSG GGSGYIPEAP RDGQ AYVRK DGEWVLLSTF LGGGSAWSHP QFEK

UniProtKB: Spike glycoprotein

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 20 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #8: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 8 / Number of copies: 3 / Formula: BLA
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

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Macromolecule #9: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 9 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 468039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

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