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Yorodumi- EMDB-33975: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33975 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | SARS-CoV-2 / spike / Antibody / IgG / Fab / VIRAL PROTEIN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Anzai I / Fujita J / Ono C / Kosaka Y / Miyamoto Y / Shichinohe S / Takada K / Torii S / Taguwa S / Suzuki K ...Anzai I / Fujita J / Ono C / Kosaka Y / Miyamoto Y / Shichinohe S / Takada K / Torii S / Taguwa S / Suzuki K / Makino F / Kajita T / Inoue T / Namba K / Watanabe T / Matsuura Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 23 items
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Citation | Journal: To Be Published Title: Characterization of an antibody that neutralizes a wide range of SARS-CoV-2 variants by recognizing a novel epitope in the loop region adjacent to the ACE2-binding interface with the receptor-binding domain Authors: Anzai I / Fujita J / Ono C / Kosaka Y / Miyamoto Y / Shichinohe S / Takada K / Torii S / Taguwa S / Suzuki K / Makino F / Kajita T / Inoue T / Namba K / Watanabe T / Matsuura Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33975.map.gz | 17 MB | EMDB map data format | |
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Header (meta data) | emd-33975-v30.xml emd-33975.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33975_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_33975.png | 156.8 KB | ||
Masks | emd_33975_msk_1.map | 178 MB | Mask map | |
Others | emd_33975_half_map_1.map.gz emd_33975_half_map_2.map.gz | 140.6 MB 140.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33975 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33975 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33975.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.861 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33975_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33975_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33975_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with...
Entire | Name: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation |
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Components |
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-Supramolecule #1: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with...
Supramolecule | Name: Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) with C480A mutation type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPA NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGSH HHHHHHH GENBANK: GENBANK: QHD43416.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.48 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE Details: The graphene grid was chemically oxidized and modified. | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2 |