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- EMDB-39371: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (2-up state) -
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Open data
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Basic information
Entry | ![]() | |||||||||||||||||||||||||||
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Title | SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (2-up state) | |||||||||||||||||||||||||||
![]() | 0.004 | |||||||||||||||||||||||||||
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![]() | Antibody / Complex / VIRAL PROTEIN | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||||||||||||||||||||
![]() | Anraku Y / Kita S / Onodera T / Tadokoro T / Ito S / Adachi Y / Kotaki R / Suzuki T / Hashiguchi T / Takahashi Y / Maenaka K | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108 Authors: Anraku Y / Maenaka K | |||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 171.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.1 KB 23.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.7 KB | Display | ![]() |
Images | ![]() | 81.2 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 171.3 MB 171.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | 0.004 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.7538 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: 0.0187
File | emd_39371_half_map_1.map | ||||||||||||
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Annotation | 0.0187 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 0.0187
File | emd_39371_half_map_2.map | ||||||||||||
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Annotation | 0.0187 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv
Entire | Name: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv
Supramolecule | Name: SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 20 KDa |
-Supramolecule #2: SARS-CoV-2 spike glycoprotein
Supramolecule | Name: SARS-CoV-2 spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: NT-108 scFv
Supramolecule | Name: NT-108 scFv / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: SARS-CoV-2 spike glycoprotein
Macromolecule | Name: SARS-CoV-2 spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: SSQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHVS GTNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG ...String: SSQCVNLTTR TQLPPAYTNS FTRGVYYPDK VFRSSVLHST QDLFLPFFSN VTWFHAIHVS GTNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GDSSSGWTAG AAAYYVGYLQ PRTFLLKYNE NGTITDAVDC ALDPLSETKC TLKSFTVEKG IYQTSNFRVQ PTESIVRFPN ITNLCPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP LQSYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLTGTGV LTESNKKFLP FQQFGRDIAD TTDAVRDPQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQDVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEHVNNSYE CDIPIGAGIC ASYQTQTNSP GSAGSVASQS IIAYTMSLGA ENSVAYSNNS IAIPTNFTIS VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGFN FSQILPDPSK PSKRSPIEDL LFNKVTLADA GFIKQYGDCL GDIAARDLIC AQKFNGLTVL PPLLTDEMIA QYTSALLAGT ITSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNQNAQALNT LVKQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSGNCDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQYI |
-Macromolecule #2: NT-108 scFv
Macromolecule | Name: NT-108 scFv / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS STFLAWYQQK PGQAPRLLIY GASYMATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSLTFG GGTKLEIKGG GGSGGGGSGG GGSQVQLQQS GPGLVKPSQT LSLTCSISGD SVSSNSAAWN W IRQSPSRG ...String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS STFLAWYQQK PGQAPRLLIY GASYMATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSLTFG GGTKLEIKGG GGSGGGGSGG GGSQVQLQQS GPGLVKPSQT LSLTCSISGD SVSSNSAAWN W IRQSPSRG LEWLGRTYYR SKWYNDYAGT VKSRIAINPD TSKNQFSLHL NSVTPEDTAV YFCARVISVA GYAFDIWGQG TM VTVSSHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: PBS | ||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blotting time 5 s and blotting force 5.. |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4792 pixel / Number real images: 2832 / Average exposure time: 1.5 sec. / Average electron dose: 53.52 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |