+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35171 | |||||||||
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Title | Omicron spike variant XBB with n3130v-Fc | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Omicron / Spike / Antibody / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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 / 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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.44 Å | |||||||||
Authors | Hao AH / Zhang X / Chen ZG / Sun L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Signal Transduct Target Ther / Year: 2023 Title: Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants. Authors: Aihua Hao / Wenping Song / Cheng Li / Xiang Zhang / Chao Tu / Xun Wang / Pengfei Wang / Yanling Wu / Tianlei Ying / Lei Sun / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35171.map.gz | 57 MB | EMDB map data format | |
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Header (meta data) | emd-35171-v30.xml emd-35171.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_35171.png | 87.8 KB | ||
Filedesc metadata | emd-35171.cif.gz | 6.2 KB | ||
Others | emd_35171_half_map_1.map.gz emd_35171_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35171 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35171 | HTTPS FTP |
-Validation report
Summary document | emd_35171_validation.pdf.gz | 639.1 KB | Display | EMDB validaton report |
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Full document | emd_35171_full_validation.pdf.gz | 638.7 KB | Display | |
Data in XML | emd_35171_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_35171_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35171 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35171 | HTTPS FTP |
-Related structure data
Related structure data | 8i4fMC 8i4eC 8i4gC 8i4hC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35171.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35171_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35171_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Omicron Spike with 6m6
Entire | Name: Omicron Spike with 6m6 |
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Components |
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-Supramolecule #1: Omicron Spike with 6m6
Supramolecule | Name: Omicron Spike with 6m6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: XBB
Supramolecule | Name: XBB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Bn03
Supramolecule | Name: Bn03 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 143.393922 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS ...String: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS SANNCTFEYV SQPFLMDLEG KEGNFKNLRE FVFKNIDGYF KIYSKHTPIN LERDLPQGFS ALEPLVDLPI GI NITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIY QTSNFR VQPTESIVRF PNITNLCPFH EVFNATTFAS VYAWNRKRIS NCVADYSVIY NFAPFFAFKC YGVSPTKLND LCFT NVYAD SFVIRGNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKPSGN YNYLYRLFRK SKLKPFERDI STEIY QAGN KPCNGVAGSN CYSPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLT ESN KKFLPFQQFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTW RV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHRRAR SVASQSIIAY TMSLGAENSV AYSNNSIA I PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTI TSGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV N HNAQALNT LVKQLSSKFG AISSVLNDIL SRLDKVEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CV LGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQ IITTDN TFVSGNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNL NESLI DLQELGKYEQ GSGYIPEAPR DGQAYVRKDG EWVFLSTFLS GLEVLFQGPG GWSHPQFEKG GGSGGGSGGS AWSHP QFEK GGSHHHHHHH H UniProtKB: Spike glycoprotein |
-Macromolecule #2: n3130v-Fc
Macromolecule | Name: n3130v-Fc / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.016805 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASDFYFD YYEMSWVRQA PGQGLEWVST ISGLGGATYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTALYYCATR SPFGDYAFSY WGQGTLVTVS SGGGGSGGGG SGGGGSGPDK THTCPPCPAP ELLGGPSVFL F PPKPKDTL ...String: EVQLVESGGG LVQPGGSLRL SCAASDFYFD YYEMSWVRQA PGQGLEWVST ISGLGGATYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTALYYCATR SPFGDYAFSY WGQGTLVTVS SGGGGSGGGG SGGGGSGPDK THTCPPCPAP ELLGGPSVFL F PPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KV SNKALPA PIEKTISKAK GQPREPQVYT LPPSRDELTK NQVSLTCLVK GFYPSDIAVE WESNGQPENN YKTTPPVLDS DGS FFLYSK LTVDKSRWQQ GNVFSCSVMH EALHNHYTQK SLSLSPGKAA ARGLNDIFEA QKIEWHE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 605011 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |