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Yorodumi- EMDB-50426: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein, with two RB... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50426 | |||||||||
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Title | SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein, with two RBD up and one RBD down. | |||||||||
Map data | unsharped map | |||||||||
Sample |
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Keywords | SARS-CoV-2 / Spike / single chain fragment / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Berlinguer M / Chaves-Sanjuan A / Milazzo FM / Minenkova O / De Santis R / Bolognesi M | |||||||||
Funding support | Italy, 1 items
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Citation | Journal: To Be Published Title: Structure of scFv76 in complex with SARS-CoV-2 Omicron Spike protein Authors: Chaves-Sanjuan A / Bolognesi M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50426.map.gz | 121.1 MB | EMDB map data format | |
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Header (meta data) | emd-50426-v30.xml emd-50426.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_50426.png | 61.1 KB | ||
Masks | emd_50426_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-50426.cif.gz | 5.8 KB | ||
Others | emd_50426_additional_1.map.gz emd_50426_half_map_1.map.gz emd_50426_half_map_2.map.gz | 230 MB 226.7 MB 226.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50426 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50426 | HTTPS FTP |
-Validation report
Summary document | emd_50426_validation.pdf.gz | 756.6 KB | Display | EMDB validaton report |
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Full document | emd_50426_full_validation.pdf.gz | 756.2 KB | Display | |
Data in XML | emd_50426_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_50426_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50426 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50426 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50426.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | unsharped map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.889 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_50426_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharped map
File | emd_50426_additional_1.map | ||||||||||||
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Annotation | sharped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50426_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50426_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
Entire | Name: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein |
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Components |
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-Supramolecule #1: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
Supramolecule | Name: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 510 KDa |
-Macromolecule #1: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein
Macromolecule | Name: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPII VPEDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSSSGW TAGAAAYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGFNC YFPLRSYSFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLKG TGVLTESNKK FLPFQQFGRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVNVFQTRAG CLIGAEYVNN SYECDIPIGA GICASYQTSQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLKRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKYFGGF NFSQILPDPS KSKRSFIEDL LFNKVTKFKG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNHNAQ ALNTLVKQLS SKFGAISSVL NDIFSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNTFVSGNCD VVIGIVNNTV YDPLQPELDS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7 / Details: PBS |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 7179 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Protocol: FLEXIBLE FIT |