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Yorodumi- EMDB-16028: Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16028 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 4, one RBD up) | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | SARS-CoV-2 / spike / Omicron / BA.1 / nanobody / W25 / VIRAL PROTEIN | |||||||||
Biological species | Homo sapiens (human) / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.97 Å | |||||||||
Authors | Modhiran N / Lauer S / Spahn CMT / Watterson D / Schwefel D | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 4, one RBD up) Authors: Schwefel D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16028.map.gz | 48.5 MB | EMDB map data format | |
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Header (meta data) | emd-16028-v30.xml emd-16028.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_16028.png | 74.2 KB | ||
Masks | emd_16028_msk_1.map | 51.4 MB | Mask map | |
Filedesc metadata | emd-16028.cif.gz | 5.9 KB | ||
Others | emd_16028_half_map_1.map.gz emd_16028_half_map_2.map.gz | 47.8 MB 47.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16028 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16028 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16028.map.gz / Format: CCP4 / Size: 51.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16028_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_16028_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_16028_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25
Entire | Name: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25
Supramolecule | Name: SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: SARS-CoV-2 spike protein (Omicron BA.1 variant)
Macromolecule | Name: SARS-CoV-2 spike protein (Omicron BA.1 variant) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL D HKNNKSWM ESEFRVYSSA NNCTFEYVSQ ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL D HKNNKSWM ESEFRVYSSA NNCTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPIIVR EP EDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENG TITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQPTESIVRF PNITNLCPFD EVFNATRFAS VYAW NRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGNI ADYNY KLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN KPCNGVAGFN CYFPLR SYS FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL KGTGVLTESN KKFLPFQ QF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTW R VYSTGSNVFQ TRAGCLIGAE YVNNSYECDI PIGAGICASY QTQTKSHRRA RSVASQSIIA YTMSLGAEN SVAYSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVF AQVKQIYKTP PIKYFGGFNF SQILPDPSKP SKRSFIEDLL FNKVTLADAG FIKQYGDCLG D IAARDLIC AQKFKGLTVL PPLLTDEMIA QYTSALLAGT ITSGWTFGAG AALQIPFAMQ MAYRFNGIGV TQ NVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNHNAQALN TLVKQLSSKF GAISSVLNDI FSR LDKVEA EVQIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFP QSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTHWFVTQRN FYEPQIITTD NTFVS GNCD VVIGIVNNTV YDPLQPELDS FKEELDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNL NES LIDLQELGKY EQYIKWPWYI WLGFIAGLIA IVMVTIMLCC MTSCCSCLKG CCSCGSCCKF DEDDSEP VL KGVKLHYT GENBANK: GENBANK: UFO69279.1 |
-Macromolecule #2: Nanobody W25
Macromolecule | Name: Nanobody W25 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKYLLPTAAA GLLLLAAQP A MAQVQLVE SG GGLVQPG ESL RLSCAA SGSI FGIYA VHWFR MAPG KEREFT AGF GSHGSTN YA ASVKGRFT M SRDNAKNTT YLQMNSLKPA DTAVYYCHA L IKNELGFL DY WGPGTQV TVS SAAAHH HHHH GAAEQ KLISE EDLN GAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9125 / Average exposure time: 3.3 sec. / Average electron dose: 40.0 e/Å2 |
-Image processing
Particle selection | Number selected: 2458527 |
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Startup model | Type of model: OTHER |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) |
Final 3D classification | Number classes: 3 / Software - Name: cryoSPARC (ver. 3.3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 32512 |