+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16441 | ||||||||||||
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Title | Omicron B.1.1.529 2 RBD up conformation | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | COVID-19 / SPIKE TRIMER / OMICRON / B.1.1.529 / VIRAL PROTEIN | ||||||||||||
Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||||||||
Biological species | Alphacoronavirus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Raghavan SSR / Walker MR / Salanti A / Barfod LK / Wang KT | ||||||||||||
Funding support | Denmark, 3 items
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Citation | Journal: To Be Published Title: Omicron B.1.1.529 2 RBD up conformation Authors: Raghavan SSR / Walker MR / Salanti A / Barfod LK / Wang KT | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16441.map.gz | 215.9 MB | EMDB map data format | |
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Header (meta data) | emd-16441-v30.xml emd-16441.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_16441.png | 76.3 KB | ||
Filedesc metadata | emd-16441.cif.gz | 5.9 KB | ||
Others | emd_16441_additional_1.map.gz emd_16441_half_map_1.map.gz emd_16441_half_map_2.map.gz | 209.9 MB 391.6 MB 391.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16441 | HTTPS FTP |
-Related structure data
Related structure data | 8c5rMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16441.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_16441_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16441_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16441_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Omicron Spike trimeric complex
Entire | Name: Omicron Spike trimeric complex |
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Components |
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-Supramolecule #1: Omicron Spike trimeric complex
Supramolecule | Name: Omicron Spike trimeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Alphacoronavirus |
Molecular weight | Theoretical: 0.4 kDa/nm |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Alphacoronavirus |
Molecular weight | Theoretical: 118.193594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LDVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE G KQGNFKNL ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISRFDN PVLPFNDGVY FASIEKSNII RGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LDVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE G KQGNFKNL REFVFKNIDG YFKIYSKHTP IIVPEDLPQG FSALEPLVDL PIGINITRFQ TLLALHRSSS GWTAGAAAYY VG YLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFDEVFNAT RFA SVYAWN RKRISNCVAD YSVLYNLAPF FTFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGNIADYNYK LPDD FTGCV IAWNSKNLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGFNCYFPLR SYSFRPTYGV GHQPY RVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLKGTGVL TESNKKFLPF QQFGRDIADT TDAVRDPQTL EILDIT PCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVN VFQTRAGCLI GAEYVNNSYE CDIPIGAGIC ASYQTSQSII AYTMSLG AE NSVAYSNNSI AIPTNFTISV TTEILPVSMT KTSVDCTMYI CGDSTECSNL LLQYGSFCTQ LKRALTGIAV EQDKNTQE V FAQVKQIYKT PPIKYFGGFN FSQILPDPSK SKRSFIEDLL FNKVTKFKGL TVLPPLLTDE MIAQYTSALL AGTITSGWT FGAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNHNAQ ALNTLVKQLS SKFGAISSV LNDIFSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG Y HLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CD VVIGIVN NTVYDPLQPE LDS UniProtKB: Spike glycoprotein |
-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: 7.5 |
Grid | Model: Homemade / Material: GRAPHENE OXIDE / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19500 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8c5r: |