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Yorodumi- EMDB-50429: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein, with two RB... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50429 | |||||||||
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Title | SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein, with two RBD up and one down. The single chain fragment scFv76-77 is bound to the two RBD up. | |||||||||
Map data | ||||||||||
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: 3.7 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 scFv76-77 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_50429.map.gz | 120.7 MB | EMDB map data format | |
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Header (meta data) | emd-50429-v30.xml emd-50429.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
Images | emd_50429.png | 61.4 KB | ||
Masks | emd_50429_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-50429.cif.gz | 6.1 KB | ||
Others | emd_50429_additional_1.map.gz emd_50429_half_map_1.map.gz emd_50429_half_map_2.map.gz | 230.2 MB 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50429 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50429 | HTTPS FTP |
-Validation report
Summary document | emd_50429_validation.pdf.gz | 870.2 KB | Display | EMDB validaton report |
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Full document | emd_50429_full_validation.pdf.gz | 869.8 KB | Display | |
Data in XML | emd_50429_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_50429_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50429 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50429 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50429.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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_50429_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharped map
File | emd_50429_additional_1.map | ||||||||||||
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Annotation | sharped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50429_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50429_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 scFv76-77 |
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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 scFv76-77 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: scFv76-77 single chain fragment
Supramolecule | Name: scFv76-77 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 HAPATV(NAG)CGP KKSTNLVKNK CVNFNFNGLK GTGVLTESNK KFLPFQQFGR DIADTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVNVFQTRA GCLIGAEYVN NSYECDIPIG AGICASYQTS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFGG FNFSQILPDP SKSKRSFIED LLFNKVTKFK GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQI PFAMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTASALG KLQDVVNHNA QALNTLVKQL SSKFGAISSV LNDIFSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFVTQ RNFYEPQIIT TDNTFVSGNC DVVIGIVNNT VYDPLQPELD S |
-Macromolecule #2: scFv76-77 single chain fragment
Macromolecule | Name: scFv76-77 single chain fragment / 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 SKDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGEK ...String: RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SKDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGEK ATLFC RASQ TFSSNY LAW YQQKPGQ AP SLLIYGGS T RAAGIPDRF SGSGSGTDFT LTINRLEPE D FAIYYCQE YG SSPRVTF GQG TRLEIK RAAA GDYKD DDDKH HHHH H |
-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: 4132 / 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 |