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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: J Virol / Year: 2025
Title: Structural and functional constraints on spike activation and host protease utilization limit cell entry of SARS-CoV-2-related bat coronaviruses.
Authors: Qingqing Li / Xiao Cai / Xiaoning Li / Yibing Zhang / Ru Li / Zirui Kang / Didi Wan / Jiaxu Wang / Lili Li / Junxia Yang / Jianxiang Shi / Shuiling Jin / Xiangdong Sun / Ying Peng / Na Zang ...Authors: Qingqing Li / Xiao Cai / Xiaoning Li / Yibing Zhang / Ru Li / Zirui Kang / Didi Wan / Jiaxu Wang / Lili Li / Junxia Yang / Jianxiang Shi / Shuiling Jin / Xiangdong Sun / Ying Peng / Na Zang / Zhengkun Xie / Yushun Wan / Jian Shang /
Abstract: The persistent threat posed by SARS-CoV-2-related coronaviruses (SC2r-CoVs) in wildlife highlights the risk of zoonotic transmission. Cross-species infectivity is predominantly determined by spike (S) ...The persistent threat posed by SARS-CoV-2-related coronaviruses (SC2r-CoVs) in wildlife highlights the risk of zoonotic transmission. Cross-species infectivity is predominantly determined by spike (S) character and S-mediated cell entry. In this study, we systematically investigated BANAL-52 and BANAL-103, which exhibit the closest genetic proximity to SARS-CoV-2, focusing on their spike structures and functional characteristics. First, despite comparable receptor-binding domain (RBD)-ACE2 interactions, the spikes of BANAL-52 and BANAL-103 displayed significantly reduced ACE2 binding compared to SARS-CoV-2, suggesting impaired S activation. Second, Cryo-EM structural analyses revealed that BANAL-52 S is stabilized in a "locked" state through linoleic acid (LA) binding and an additional N370 glycan, whereas BANAL-103 S adopts a "closed" conformation due to a unique glycan network. Site-directed mutagenesis targeting the LA binding pocket confirmed that Y365 is related to S conformational transitions and viral entry. Third, both BANAL spikes relied predominantly on lysosomal proteases (e.g., cathepsins) for membrane fusion, unlike SARS-CoV-2, which utilizes a broader range of proteases (e.g., TMPRSS2 and furin). The introduction of a furin cleavage site enhanced the fusogenicity of BANAL spikes. Finally, sera from individuals who have recovered from SARS-CoV-2 effectively neutralized BANAL pseudoviruses, underscoring conserved antigenicity. Our findings elucidate structural and proteolytic barriers that restrict the zoonotic potential of these viruses and propose targeted surveillance strategies to preempt the emergence of SC2r-CoVs.
IMPORTANCE: The viral entry mechanisms, which are primarily related to the spike character, play a critical role in determining zoonotic potential. Among the currently identified SC2r-CoVs, BANAL-52 ...IMPORTANCE: The viral entry mechanisms, which are primarily related to the spike character, play a critical role in determining zoonotic potential. Among the currently identified SC2r-CoVs, BANAL-52 and BANAL-103 exhibit spike proteins with the highest sequence similarity to SARS-CoV-2, rendering them optimal models for comparative studies on S-mediated cell entry and cross-species transmission. In this study, we systematically investigated the molecular constraints governing the functionality of BANAL spikes, with a focus on S-ACE2 interactions, S activation, S structures, and host protease utilization. Notably, we resolved the cryo-EM structure of BANAL-52 S at neutral pH and the first cryo-EM structure of BANAL-103 S, revealing distinct glycan- and lipid-mediated stabilization of inactive states. Furthermore, cross-neutralization assays demonstrated that sera of convalescents from SARS-CoV-2 inhibited BANAL pseudovirus entry with an efficiency of approximately 80%, thereby highlighting conserved antigenic epitopes and informing the development of broad-spectrum therapeutic strategies against emerging SC2r-CoVs.
History
DepositionOct 23, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 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
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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

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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

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62145_half_map_2.map
Projections & Slices
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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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