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- EMDB-61170: Cryo-EM structure of Bat SARS-like coronavirus Khosta-1 spike protein -

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Basic information

Entry
Database: EMDB / ID: EMD-61170
TitleCryo-EM structure of Bat SARS-like coronavirus Khosta-1 spike protein
Map data
Sample
  • Complex: Spike protein of Bat SARS-like coronavirus Khosta-1
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsKhosta-1 / 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 / 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 ...Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Bat SARS-like coronavirus Khosta-1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 15, 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_61170.png

Downloads & links

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Map

FileDownload / File: emd_61170.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 480 pix.
= 331.2 Å		0.69 Å/pix.
x 480 pix.
= 331.2 Å		0.69 Å/pix.
x 480 pix.
= 331.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.41584638 - 0.87158024
Average (Standard dev.)-0.00009655452 (±0.026233263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61170_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #2

Fileemd_61170_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_61170_half_map_2.map
Projections & Slices
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Sample components

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Entire : Spike protein of Bat SARS-like coronavirus Khosta-1

EntireName: Spike protein of Bat SARS-like coronavirus Khosta-1
Components
  • Complex: Spike protein of Bat SARS-like coronavirus Khosta-1
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

SupramoleculeName: Spike protein of Bat SARS-like coronavirus Khosta-1 / 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-1
Molecular weightTheoretical: 128.727352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFFIFLSFL PLITAQEGCG VLSNKSTPNL DQFLSSRRGF YYFDDTFRSS VRVLTSGYFL PFQSNLTRYL TLESITGRRI YFDNPNIPF KDGLYFAATE KSNVIRGWIF GSTLDNTTQS AVLFNNGTHI VVNVCNFNFC QDPMLAISAG SPYKSWVYTT A TNCTYNRL ...String:
MKFFIFLSFL PLITAQEGCG VLSNKSTPNL DQFLSSRRGF YYFDDTFRSS VRVLTSGYFL PFQSNLTRYL TLESITGRRI YFDNPNIPF KDGLYFAATE KSNVIRGWIF GSTLDNTTQS AVLFNNGTHI VVNVCNFNFC QDPMLAISAG SPYKSWVYTT A TNCTYNRL HAFNISTSIN PGSFVHLREH VFRNVDGFLY VYHNYESINV TNTFPGGFSV LKPILKLPFG LNITHFKVIM TL FSNTTQS FEADASAYFV GHLKPLTMLA DFDENGTIVD AVDCSQNPLS ELKCTTKSFS VEKGIYQTSN FRVSPSTEVV RFP NITNLC PFGQVFNAST FPSVYAWGRM RISDCVADYS VLYNSTSSFS TFKCYGVSPT KLNDLCFSSV YADYFVVKGD DVRQ IAPAQ TGVIADYNYK LPDDFTGCVL AWNTKSIDKG QGFYYRLFRH GKIKPYERDT SNVPYNAQGG TCTDTSQLNC YQPLK SYDF TDTVGVGYQP YRVVVLSFEL LNAPATVCGP KQSTELVKNK CVNFNFNGLT GTGVLTESTK RFQSFQQFGR DISDFT DSV RDPKTLEILD ISPCSYGGVS VITPGTNASN VVAVLYQDVN CTDVPTMLHT EQVAHDWRVY AVNTDGNMFQ TQAGCLV GA TYENTSYECD IPIGAGVCAK FGSTKTRQQS ILAYTMSIGE DQSVAYSNNS IAIPTNFSIS VTTEVLPVSM TKTSVDCN M YICGDSTECS NLLLQYGSFC TQLNRALSGI AVEQDRNTRD VFAQTKTIYK TPNIKDFGGF NFSQILPDPG KPSQRSPIE DLLYNKVTLA DPGFMKQYGD CLGGINARDL ICAQKFNGLT VLPPLLTDDM IAAYTAALIS GTATAGYTFG AGPALQIPFP MQMAYRFNG IGVTQNVLYE NQKQIANQFN KAISQIQDSL TTTPTALGKL QDVINQNAAA LNTLVKQLSS NFGAISSVLN D ILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HLMSFPQAAP HG VVFLHVT YVPSEQKNFT TAPAICHNGK AYFPKEGVFV MNGTHWFITQ RNFYSPQVIT TDNTFESGTC DVVIGIVNNT VYG GGSGGG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGG GSAWSHPQFE K

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: 32 / 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: 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 312075
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

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