+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27205 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Closed state of SARS-CoV-2 BA.2 variant spike protein | |||||||||||||||||||||
Map data | The overall map of SARS-CoV-2 BA2 variant closed state | |||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Keywords | VIRAL PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||||||||
Authors | Zhang J / Tang WC / Gao HL / Shi W / Peng HQ / Volloch SR / Xiao TS / Chen B | |||||||||||||||||||||
Funding support | United States, 6 items
| |||||||||||||||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Authors: Jun Zhang / Weichun Tang / Hailong Gao / Christy L Lavine / Wei Shi / Hanqin Peng / Haisun Zhu / Krishna Anand / Matina Kosikova / Hyung Joon Kwon / Pei Tong / Avneesh Gautam / Sophia Rits- ...Authors: Jun Zhang / Weichun Tang / Hailong Gao / Christy L Lavine / Wei Shi / Hanqin Peng / Haisun Zhu / Krishna Anand / Matina Kosikova / Hyung Joon Kwon / Pei Tong / Avneesh Gautam / Sophia Rits-Volloch / Shaowei Wang / Megan L Mayer / Duane R Wesemann / Michael S Seaman / Jianming Lu / Tianshu Xiao / Hang Xie / Bing Chen / Abstract: The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. Here, we have characterized structural, ...The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. Here, we have characterized structural, functional and antigenic properties of the full-length BA.2 spike (S) protein and compared replication of the authentic virus in cell culture and an animal model with previously prevalent variants. BA.2 S can fuse membranes slightly more efficiently than Omicron BA.1, but still less efficiently than other previous variants. Both BA.1 and BA.2 viruses replicated substantially faster in animal lungs than the early G614 (B.1) strain in the absence of pre-existing immunity, possibly explaining the increased transmissibility despite their functionally compromised spikes. As in BA.1, mutations in the BA.2 S remodel its antigenic surfaces, leading to strong resistance to neutralizing antibodies. These results suggest that both immune evasion and replicative advantage may contribute to the heightened transmissibility of the Omicron subvariants. | |||||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27205.map.gz | 321.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27205-v30.xml emd-27205.xml | 22 KB 22 KB | Display Display | EMDB header |
Images | emd_27205.png | 93 KB | ||
Others | emd_27205_additional_1.map.gz emd_27205_half_map_1.map.gz emd_27205_half_map_2.map.gz | 203.2 MB 333.3 MB 332.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27205 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27205 | HTTPS FTP |
-Related structure data
Related structure data | 8d55MC 8d56C 8d5aC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_27205.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The overall map of SARS-CoV-2 BA2 variant closed state | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: the top region map of SARS-CoV-2 BA2 variant with top region mask
File | emd_27205_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | the top region map of SARS-CoV-2 BA2 variant with top region mask | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Closed state of SARS-CoV-2 BA.2 variant spike protein
File | emd_27205_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Closed state of SARS-CoV-2 BA.2 variant spike protein | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Closed state of SARS-CoV-2 BA.2 variant spike protein
File | emd_27205_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Closed state of SARS-CoV-2 BA.2 variant spike protein | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Closed state of pre-fusion SARS-CoV-2 BA.2 variant spike protein
Entire | Name: Closed state of pre-fusion SARS-CoV-2 BA.2 variant spike protein |
---|---|
Components |
|
-Supramolecule #1: Closed state of pre-fusion SARS-CoV-2 BA.2 variant spike protein
Supramolecule | Name: Closed state of pre-fusion SARS-CoV-2 BA.2 variant spike protein type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Closed state of pre-fusion SARS-CoV-2 BA.2 variant spike protein |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 600 kDa/nm |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 144.688156 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV ...String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LGRDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIR GNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHRRAR SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIL SRLDKVEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ YIKWPWYIWL GFIAGLIAIV MVTIMLCCMT SCCSCLKGCC SCGSCCKFDE DDSEPVLKGV KLHYTSGGGS AWSHP QFEK GGGSGGGSGG SSAWSHPQFE K UniProtKB: Spike glycoprotein |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 21 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.853 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 6763049 |
---|---|
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 160774 |