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- EMDB-66900: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-66900
TitleSarbecovirus GX2013 Spike S1 in complex with C092 Fab
Map data
Sample
  • Complex: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab
    • Protein or peptide: Heavy chain of C092 Fab
    • Protein or peptide: Light chain of C092 Fab
    • Protein or peptide: Spike glycoprotein
KeywordsSpike protein / Antibody Fab fragment / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 ...positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 S2 superfamily, coronavirus / 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 speciesBtRs-BetaCoV/GX2013 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsNiu C / Liu B / Gao X / Li Z / He J / Xiong X
Funding support China, 8 items
OrganizationGrant numberCountry
Other government2021YFA1300903
National Natural Science Foundation of China (NSFC)82341085 China
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2021A1515011289
Other government2023B1212060050
Other government2023B1212120009
Other governmentGIBHBRP24-02
CitationJournal: To Be Published
Title: AI identifies Elite Antibodies that Tolerate Escape Mutations from a Population Antibody Class Exerting Continued Selection Over SARS-CoV-2
Authors: Niu C / Huang X / Yan Q / Liu B / Gao X / Song Y / Wang J / Wang L / Li Z / Zheng H / He P / Huang X / Yuan H / Zou B / Yang Y / Wu F / Yao Y / Chen X / Chen L / He J / Yao J / Zhao J / Xiong X
History
DepositionNov 2, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66900.png

Downloads & links

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Map

FileDownload / File: emd_66900.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 192 pix.
= 253.44 Å		1.32 Å/pix.
x 192 pix.
= 253.44 Å		1.32 Å/pix.
x 192 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.8973922 - 2.780384
Average (Standard dev.)0.001268265 (±0.051457062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66900_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_66900_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 : Sarbecovirus GX2013 Spike S1 in complex with C092 Fab

EntireName: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab
Components
  • Complex: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab
    • Protein or peptide: Heavy chain of C092 Fab
    • Protein or peptide: Light chain of C092 Fab
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab

SupramoleculeName: Sarbecovirus GX2013 Spike S1 in complex with C092 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: BtRs-BetaCoV/GX2013 (virus)

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Macromolecule #1: Heavy chain of C092 Fab

MacromoleculeName: Heavy chain of C092 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.114055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGSFT NHFISWVRQA PGQGLEWMGR IIPILGTANY AQNFQGRVMM TADKSTSTAY MELSSLRSE DTAVYYCARD SGYSGYGSTY YMDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGSFT NHFISWVRQA PGQGLEWMGR IIPILGTANY AQNFQGRVMM TADKSTSTAY MELSSLRSE DTAVYYCARD SGYSGYGSTY YMDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD

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Macromolecule #2: Light chain of C092 Fab

MacromoleculeName: Light chain of C092 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.886127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SGAPGQRVTI SCTGSNSNIG AGYDVHWYQQ LPGAAPKLLI YGNNNRPSGV PDRFSGSKSD TSASLAITGL QVEDEADYY CQSYDSSLSD SVFGSGTKVT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSVLTQPPSV SGAPGQRVTI SCTGSNSNIG AGYDVHWYQQ LPGAAPKLLI YGNNNRPSGV PDRFSGSKSD TSASLAITGL QVEDEADYY CQSYDSSLSD SVFGSGTKVT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: BtRs-BetaCoV/GX2013 (virus)
Molecular weightTheoretical: 139.117812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKILILAFLA SLAKAQEGCG IISRKPQPKM AQVSSSRRGV YYNDDIFRSD VLHLTQDYFL PFDSNLTQYF SLNVDSDRYT YFDNPILDF GDGVYFAATE KSNVIRGWIF GSSFDNTTQS AVIVNNSTHI IIRVCNFNLC KEPMYTVSRG TQQNSWVYQS A FNCTYDRV ...String:
MKILILAFLA SLAKAQEGCG IISRKPQPKM AQVSSSRRGV YYNDDIFRSD VLHLTQDYFL PFDSNLTQYF SLNVDSDRYT YFDNPILDF GDGVYFAATE KSNVIRGWIF GSSFDNTTQS AVIVNNSTHI IIRVCNFNLC KEPMYTVSRG TQQNSWVYQS A FNCTYDRV EKSFQLDTAP KTGNFKDLRE YVFKNRDGFL SVYQTYTAVN LPRGLPQGFS VLRPILKLPF GINITSYRVV MA MFSQSTS NFLPESAAYY VGNLKYSTFM LSFNENGTIT DAIDCSQNPL AELKCTIKNF NVNKGIYQTS NFRVSPTQEV VRF PNITNR CPFDKVFNAT RFPNVYAWER TKISDCVADY TVLYNSTSFS TFKCYGVSPS KLIDLCFTSV YADTFLIRSS EVRQ VAPGE TGVIADYNYK LPDDFTGCVI AWNTAKQDTG NYYYRSHRKT KLKPFERDLS SDDGNGVYTL STYDFNPNVP VAYQA TRVV VLSFELLNAP ATVCGPKLST QLVKNQCVNF NFNGLKGTGV LTPSLKRFQS FQQFGRDTSD FTDSVRDPQT LEILDI SPC SFGGVSVITP GTNASSEVAV LYQDVNCTDV PTAIRADQLT PAWRVYSTGL NVFQTQAGCL IGAEHVNASY ECDIPIG AG ICASYHTASV LRSTGQKSIV AYTMSLGAEN SIAYANNSIA IPTNFSISVT TEVMPVSMAK TSVDCTMYIC GDSLECSN L LLQYGSFCTQ LNRALTGIAI EQDKNTQEVF AQVKQMYKTP AIKDFGGFNF SQILPDPSKP TKRSFIEDLL FNKVTLADA GFMKQYGECL GDISARDLIC AQKFNGLTVL PPLLTDEMIA AYTAALVSGT ATAGWTFGAG AALQIPFAMQ MAYRFNGIGV TQNVLYENQ KQIANQFNKA ISQIQESLTT TSTALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDKVEAE V QIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFPQAAPHG VVFLHVTYVP SQ ERNFTTA PAICHEGKAY FPREGVFVSN GTSWFITQRN FYSPQLITTD NTFVSGNCDV VIGIINNTVY DPLQPELDSF KDE LDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQELGKYE QGSGYIPEAP RDGQAYVRKD GEWV LLSTF LLEVLFQGPG HHHHHHHHSA WSHPQFEKGG GSGGGGSGGS AWSHPQFEKS A

UniProtKB: Spike glycoprotein

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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 / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8zy6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 385893
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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