[English] 日本語
![](img/lk-miru.gif)
- EMDB-38498: Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P) ... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | SARS-CoV-2 / Omicron / EG.5.1 / spike protein / human ACE2 / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex | |||||||||
Function / homology | ![]() positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / 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 / Potential therapeutics for SARS / 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 / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / 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 / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
![]() | Li LJ / Gu YH / Shi KY / Qi JX / Gao GF | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Authors: Linjie Li / Kaiyuan Shi / Yuhang Gu / Zepeng Xu / Chang Shu / Dedong Li / Junqing Sun / Mengqing Cong / Xiaomei Li / Xin Zhao / Guanghui Yu / Songnian Hu / Hui Tan / Jianxun Qi / Xiaopeng Ma ...Authors: Linjie Li / Kaiyuan Shi / Yuhang Gu / Zepeng Xu / Chang Shu / Dedong Li / Junqing Sun / Mengqing Cong / Xiaomei Li / Xin Zhao / Guanghui Yu / Songnian Hu / Hui Tan / Jianxun Qi / Xiaopeng Ma / Kefang Liu / George F Gao / ![]() Abstract: The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2. ...The recently emerged BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 variants have a growth advantage. In this study, we explore the structural bases of receptor binding and immune evasion for the Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Our findings reveal that BA.2.86 exhibits strong receptor binding, whereas its JN.1 sub-lineage displays a decreased binding affinity to human ACE2 (hACE2). Through complex structure analyses, we observed that the reversion of R493Q in BA.2.86 receptor binding domain (RBD) plays a facilitating role in receptor binding, while the L455S substitution in JN.1 RBD restores optimal affinity. Furthermore, the structure of monoclonal antibody (mAb) S309 complexed with BA.2.86 RBD highlights the importance of the K356T mutation, which brings a new N-glycosylation motif, altering the binding pattern of mAbs belonging to RBD-5 represented by S309. These findings emphasize the importance of closely monitoring BA.2.86 and its sub-lineages to prevent another wave of SARS-CoV-2 infections. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 334.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
Images | ![]() | 85.1 KB | ||
Masks | ![]() | 669.9 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() | 587.2 MB 622.2 MB 622.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xn5MC ![]() 8xlvC ![]() 8xm5C ![]() 8xmgC ![]() 8xmtC ![]() 8xn2C ![]() 8xn3C ![]() 8xnfC ![]() 8xnkC ![]() 8y16C ![]() 8y18C ![]() 8y5jC ![]() 8y6aC 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: 0.808 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: sharpen map
File | emd_38498_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpen map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_38498_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_38498_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2
Entire | Name: SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2 |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2
Supramolecule | Name: SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Angiotensin-converting enzyme 2
Macromolecule | Name: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 69.982562 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL ...String: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL KNEMARANHY EDYGDYWRGD YEVNGVDGYD YSRGQLIEDV EHTFEEIKPL YEHLHAYVRA KLMNAYPSYI SP IGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD AMVDQAWDAQ RIFKEAEKFF VSVGLPNMTQ GFWENSMLTD PGN VQKAVC HPTAWDLGKG DFRILMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LSPDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVSNDYSF IRYYTRTLYQ FQFQEALCQA AKHEGPLHKC DISNSTEAGQ KLFNMLRLGK SEPWTLALEN VVGAKN MNV RPLLNYFEPL FTWLKDQNKN SFVGWSTDWS PYADHHHHHH UniProtKB: Angiotensin-converting enzyme 2 |
-Macromolecule #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Details: Omicron EG.5.1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 136.397156 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VNLITRTQSY TNSFTRGVYY PDKVFRSSVL HSTHDLFLPF FSNVTWFHAI HVSGTNGTKR FDNPALPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYQKN NKSWMESEFR VYSSANNCTF EYVSQPFLMD L EGKEGNFK ...String: VNLITRTQSY TNSFTRGVYY PDKVFRSSVL HSTHDLFLPF FSNVTWFHAI HVSGTNGTKR FDNPALPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYQKN NKSWMESEFR VYSSANNCTF EYVSQPFLMD L EGKEGNFK NLREFVFKNI DGYFKIYSKH TPINLERDLP QGFSALEPLV DLPIGINITR FQTLLALHRS YLTPVDSSSG WT AGAAAYY VGYLQPRTFL LKYNENGTIT DAVDCALDPL SETKCTLKSF TVEKGIYQTS NFRVQPTESI VRFPNITNLC PFH EVFNAT TFASVYAWNR KRISNCVADY SVIYNFAPFF AFKCYGVSPT KLNDLCFTNV YADSFVIRGN EVSQIAPGQT GNIA DYNYK LPDDFTGCVI AWNSNKLDSK PSGNYNYLYR LLRKSKLKPF ERDISTEIYQ AGNKPCNGVA GPNCYSPLQS YGFRP TYGV GHQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLTGTGVLT ESNKKFLPFQ QFGRDIADTT DAVRDP QTL EILDITPCSF GGVSVITPGT NTSNQVAVLY QGVNCTEVPV AIHADQLTPT WRVYSTGSNV FQTRAGCLIG AEYVNNS YE CDIPIGAGIC ASYQTQTKSH GSASSVASQS IIAYTMSLGA ENSVAYSNNS IAIPTNFTIS VTTEILPVSM TKTSVDCT M YICGDSTECS NLLLQYGSFC TQLKRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKYFGGF NFSQILPDPS KPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL ICAQKFNGLT VLPPLLTDEM IAQYTSALLA GTITSGWTFG AGPALQIPFP MQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL SSTPSALGKL QDVVNHNAQA LNTLVKQLSS KFGAISSVLN D ILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HLMSFPQSAP HG VVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFVTQ RNFYEPQIIT TDNTFVSGNC DVVIGIVNNT VYD PLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQGYIPEAP RDGQ AYVRK DGEWVLLSTF LAHHHHHHHH HH 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: 36 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 403003 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |