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- EMDB-62145: SARS-CoV-2 related bat coronavirus BANAL-103 spike in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-62145
TitleSARS-CoV-2 related bat coronavirus BANAL-103 spike in the closed state
Map data
Sample
  • Complex: BANAL-103 coronavirus spike
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 related coronavirus / BANAL-103 / Spike / VIRAL PROTEIN
Biological speciesCoronaviridae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsQingqing L / Xiao C / Xiaoning L / Yibing Z / Ru L / Zirui K / Didi W / Jiaxu W / Lili L / Junxia Y ...Qingqing L / Xiao C / Xiaoning L / Yibing Z / Ru L / Zirui K / Didi W / Jiaxu W / Lili L / Junxia Y / Jianxiang S / Shuiling J / Ying P / Na Z / Yushun W / Jian S
Funding support China, 2 items
OrganizationGrant numberCountry
Other government32200113
Other government232301420013 China
CitationJournal: To Be Published
Title: Characteristics of Spike Structure, Receptor Recognition and Membrane Fusion Revealed Limitations for SARS-CoV-2 related Coronavirus Cell Entry
Authors: Qingqing L / Xiao C / Xiaoning L / Yibing Z / Ru L / Zirui K / Didi W / Jiaxu W / Lili L / Junxia Y / Jianxiang S / Shuiling J / Ying P / Na Z / Yushun W / Jian S
History
DepositionOct 23, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62145.png

Downloads & links

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Map

FileDownload / File: emd_62145.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.089342885 - 0.1364713
Average (Standard dev.)0.00016391954 (±0.003299466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62145_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62145_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 : BANAL-103 coronavirus spike

EntireName: BANAL-103 coronavirus spike
Components
  • Complex: BANAL-103 coronavirus spike
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BANAL-103 coronavirus spike

SupramoleculeName: BANAL-103 coronavirus spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Coronaviridae (virus)

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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: Coronaviridae (virus)
Molecular weightTheoretical: 137.961562 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MLFFFFLCFA SVNSQCVNLT GRATIQPSFT NSSHRGVYYP DTIFRSNSLV LSQGYFLPFY SNISWYYALT KTNGAEKRVD NPILDFKDG IYFAATEKSN IVRGWIFGTT LDNTSQSLLI VNNATNVIIK VCNFQFCYDP YLSGYFHNNK TWSTREFAVY S SYANCTFE ...String:
MLFFFFLCFA SVNSQCVNLT GRATIQPSFT NSSHRGVYYP DTIFRSNSLV LSQGYFLPFY SNISWYYALT KTNGAEKRVD NPILDFKDG IYFAATEKSN IVRGWIFGTT LDNTSQSLLI VNNATNVIIK VCNFQFCYDP YLSGYFHNNK TWSTREFAVY S SYANCTFE YVSKPFMLDI SGKSGLFDTL REFVFRNVDG YFKIYSKYSP VNVNSNLPTG FSALEPLVEL PAGINITRFR TL LTIHRGD PMPNNGWTVF SAAYYVGYLA PRTFMLKYNE NGTITDAVDC SLDPLSEAKC TLKSFTVEKG IYQTSNFRVQ PTD SIVRFP NITNLCPFGE VFNATTFASV YAWNRKRISN CVADYSVLYN STSFSTFKCY GVSPTKLNDL CFTNVYADSF VVRG DEVRQ IAPGQTGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLYRLFRKS NLKPFERDIS TEIYQAGSTP CNGVE GFNC YFPLQSYGFH PTNGVGYQPY RVVVLSFELL NAPATVCGPK KSTNLIKNKC VNFNFNGLTG TGVLTESNKK FLPFQQ FGR DIADTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNASNQ VAVLYQDVNC TEVPVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEHV NNSYECDIPI GAGICASYQT QTNSRSVASQ SIIAYTMSLG AQNSVAYSNN SIAIPTNFTI SVTTEILP V SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPQIKDFGG FNFSQILPD PSKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNQNAQ ALNTLVKQLS S NFGAISSV LNDILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YH LMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDV VIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQ YIKGS GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG HHHHHHHH

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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: 60 / 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
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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52916
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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