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Yorodumi- EMDB-50425: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein, with two RB... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50425 | |||||||||
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Title | SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein, with two RBD up and one RBD down. Single chain fragment scFv76 bound to the two RBD up | |||||||||
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 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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_50425.map.gz | 120.9 MB | EMDB map data format | |
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Header (meta data) | emd-50425-v30.xml emd-50425.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
Images | emd_50425.png | 63.9 KB | ||
Masks | emd_50425_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-50425.cif.gz | 6.1 KB | ||
Others | emd_50425_additional_1.map.gz emd_50425_half_map_1.map.gz emd_50425_half_map_2.map.gz | 230.1 MB 226.7 MB 226.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50425 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50425 | HTTPS FTP |
-Validation report
Summary document | emd_50425_validation.pdf.gz | 795.5 KB | Display | EMDB validaton report |
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Full document | emd_50425_full_validation.pdf.gz | 795.1 KB | Display | |
Data in XML | emd_50425_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_50425_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50425 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50425 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50425.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | unsharped map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_50425_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharped map
File | emd_50425_additional_1.map | ||||||||||||
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Annotation | sharped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50425_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50425_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Spike protein in complex with the single chain fragmen...
Entire | Name: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike protein in complex with the single chain fragmen...
Supramolecule | Name: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 510 KDa |
-Supramolecule #2: 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: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: scFv76 single chain fragment
Supramolecule | Name: scFv76 single chain fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-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 |
-Macromolecule #2: Single chain fragment scFv76
Macromolecule | Name: Single chain fragment scFv76 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SRDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGER ...String: RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SRDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGER ATLSC RASQ SVSSSY LAW YQQKPGQ AP RLLIYGAS S RATGIPDRF SGSGSGTDFT LTISRLEPE D FAVYYCQQ YG SSPYTFG QGT KLEIKR AAAG DYKDD DDKHH HHHH |
-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 |