+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | BA.2.86 Spike Trimer with ins483V mutation (1 RBD up) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Trimer / VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.82 Å | |||||||||
![]() | Yue C / Liu P | |||||||||
Funding support | 1 items
| |||||||||
![]() | ![]() Title: Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Authors: Liu P / Yue C / Meng B / Xiao T / Yang S / Liu S / Jian F / Zhu Q / Yu Y / Ren Y / Wang P / Li Y / Wang J / Mao X / Shao F / Wang Y / Gupta RK / Cao Y / Wang X | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 97.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.6 KB 14.6 KB | Display Display | ![]() |
Images | ![]() | 58.5 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 95.7 MB 95.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8x50MC ![]() 8whsC ![]() 8whuC ![]() 8whvC ![]() 8whwC ![]() 8whzC ![]() 8x4hC ![]() 8x4zC ![]() 8x55C ![]() 8x56C ![]() 8x5qC ![]() 8x5rC ![]() 8xurC ![]() 8xusC ![]() 8xutC ![]() 8xuuC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_38057_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_38057_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Severe acute respiratory syndrome coronavirus 2
Entire | Name: ![]() ![]() |
---|---|
Components |
|
-Supramolecule #1: Severe acute respiratory syndrome coronavirus 2
Supramolecule | Name: Severe acute respiratory syndrome coronavirus 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 134.140281 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ATMFVFLVLL PLVSSQCVMP LFNLITTTQS YTNSFTRGVY YPDKVFRSSV LHLTQDLFLP FFSNVTWFHA ISGTNGTKRF DNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVFI KVCEFQFCND PFLDVYHKNN KSWMESESGV Y SSANNCTF ...String: ATMFVFLVLL PLVSSQCVMP LFNLITTTQS YTNSFTRGVY YPDKVFRSSV LHLTQDLFLP FFSNVTWFHA ISGTNGTKRF DNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVFI KVCEFQFCND PFLDVYHKNN KSWMESESGV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PIIGRDFPQG FSALEPLVDL PIGINITRFQ TL LALNRSY LTPGDSSSGW TAGAADYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQ PTESIV RFPNVTNLCP FHEVFNATRF ASVYAWNRTR ISNCVADYSV LYNFAPFFAF KCYGVSPTKL NDLCFTNVYA DSFV IKGNE VSQIAPGQTG NIADYNYKLP DDFTGCVIAW NSNKLDSKHS GNYDYWYRLF RKSKLKPFER DISTEIYQAG NKPCK GVKG PNCYFPLQSY GFRPTYGVGH QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLTKS NKKFLP FQQ FGRDIVDTTD AVRDPQTLEI LDITPCSFGG VSVITPGTNT SNQVAVLYQG VNCTEVSVAI HADQLTPTWR VYSTGSN VF QTRAGCLIGA EYVNNSYECD IPIGAGICAS YQTQTKSRRA AASVASQSII AYTMSLGAEN SVAYSNNSIA IPTNFTIS V TTEILPVSMT KTSVDCTMYI CGDSTECSNL LLQYGSFCTQ LKRALTGIAV EQDKNTQEVF AQVKQIYKTP PIKYFGGFN FSQILPDPSK PSKRSPIEDL LFNKVTLADA GFIKQYGDCL GDIAARDLIC AQKFNGLTVL PPLLTDEMIA QYTSALLAGT ITSGWTFGA GPALQIPFPM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLFS TPSALGKLQD VVNHNAQALN T LVKQLSSK FGAISSVLND ILSRLDPPEA EVQIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VD FCGKGYH LMSFPQSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTHWFVTQRN FYEPQIITTD NTF VSGNCD VVIGIVNNTV YDPLQLELDS FKEELDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQ ELGKY EQ UniProtKB: Spike glycoprotein |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 31 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
-
Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65569 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |