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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | SARS-CoV-2 BA-2.87.1 Spike ectodomain | |||||||||
![]() | BA2-87.1 cryoEM map C3 symmetry | |||||||||
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![]() | Viral protein / immune system / SARS-CoV-2 / RBD / Spike / glycoprotein / BA.2.87.1 / receptor / coronavirus-2 / N-terminal domain / Supersite | |||||||||
Function / homology | ![]() virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Ren J / Stuart DI / Duyvesteyn HME | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Concerted deletions eliminate a neutralising supersite in SARS-CoV-2 BA.2.87.1 spike Authors: Stuart DI / Ren J #1: ![]() Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Authors: Liebschner D / Afonine PV #2: ![]() Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Authors: Punjani A / Rubinstein JL | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 151.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
Images | ![]() | 85.5 KB | ||
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() | 147.6 MB 151 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f9yMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | BA2-87.1 cryoEM map C3 symmetry | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.7303 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: BA2-87.1 cryoEM half map C3 symmetry
File | emd_50263_half_map_1.map | ||||||||||||
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Annotation | BA2-87.1 cryoEM half map C3 symmetry | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BA2-87.1 cryoEM half map C3 symmetry
File | emd_50263_half_map_2.map | ||||||||||||
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Annotation | BA2-87.1 cryoEM half map C3 symmetry | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : BA-2.87.1 variant SARS-CoV2 S protein
Entire | Name: BA-2.87.1 variant SARS-CoV2 S protein |
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Components |
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-Supramolecule #1: BA-2.87.1 variant SARS-CoV2 S protein
Supramolecule | Name: BA-2.87.1 variant SARS-CoV2 S protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Spike protein recombinantly expressed using sequence of human-derived BA-2.87.1 variant of SARS-CoV2. |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 139.502484 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFVFLVLLPL VSSQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAISGTN DTKRFDNPVL PFNDGVYFAS TEKFNIIRG WIFGTTLDSK TQSLLIVNNA TNAVIKVCEF QFKNNKSLME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLSEFV ...String: MFVFLVLLPL VSSQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAISGTN DTKRFDNPVL PFNDGVYFAS TEKFNIIRG WIFGTTLDSK TQSLLIVNNA TNAVIKVCEF QFKNNKSLME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLSEFV FKNIDGYFKI YSKHTPINLG RGLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AY YVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNLCPFDEVF NAT RFASVY AWNRKRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IRGNEVSQIA PGQTGTIADY NYKL PDDFT GCVIAWNSNK LDSNGGGNYN YMYRLFRKSK LKPFERDIST EIYQAGNTPC KGVAGFNCYF PLQSYGFRPT YGVGH QPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQFGRDI ADTTDAVRDP QTLEIL DIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVSVAIHADQ LTPTWRVYST GSNGFQTRAG CLIGAEYVNN SYECDIP IG AGICASYQTQ TRSHGSASSV ASQPIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTSVD CTMYICGD S TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKIPPIKH FGGFNFSQIL PDPSKPSKRS FIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGAALQ IPFAMQMAYR FNGIGVTQN VLYENQKLIA NQFNSAIGKI QGSLSSTASA LGKLQDVVNH NAQALNTLVK QLSSKFGAIS SVLNDILSRL D PPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HV TYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNNTVYDPLQ PEL DSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQGSG YIPEAPRDGQ AYVR KDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHGSA WSHPQFEKGG GSGGGSGGSA WSHPQFEK UniProtKB: Spike glycoprotein, Fibritin |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 39 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE |
Details | BA.2.87.1 Spike |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9818 / Average electron dose: 40.0 e/Å2 / Details: Images were collected in EER format. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |