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- EMDB-60105: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head... -
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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry) | ||||||||||||
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![]() | Spike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
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 / 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 / membrane fusion / 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 | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.45 Å | ||||||||||||
![]() | Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L ...Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L / Zhao J / Xiong X | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants Authors: Yan Q / Gao X / Liu B / Hou R / He P / Ma Y / Zhang Y / Zhang Y / Li Z / Chen Q / Wang J / Huang X / Liang H / Zheng H / Yao Y / Chen X / Niu X / He J / Chen L / Zhao J / Xiong X | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 26.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 35.5 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 48.9 MB 48.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8zhjMC ![]() 8zhdC ![]() 8zheC ![]() 8zhfC ![]() 8zhgC ![]() 8zhhC ![]() 8zhiC ![]() 8zhkC ![]() 8zhlC ![]() 8zhmC ![]() 8zhnC ![]() 8zhoC ![]() 8zhpC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60105_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60105_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head...
Entire | Name: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry) |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head...
Supramolecule | Name: SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: SARS-CoV-2 spike trimer (6P)
Supramolecule | Name: SARS-CoV-2 spike trimer (6P) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: H18 Fab
Supramolecule | Name: H18 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Spike glycoprotein,Fibritin,Expression Tag
Macromolecule | Name: Spike glycoprotein,Fibritin,Expression Tag / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 141.253875 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV YSSANNCTFE Y VSQPFLMD ...String: VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV YSSANNCTFE Y VSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QTLLALHRSY LT PGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRVQPTESIV RFP NITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQI APGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPCNGVEG FNCYF PLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFLPFQQ FGRDIA DTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCL IG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTISV TTEILPVS M TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGFN FSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL NTLVKQLSSN F GAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH LM SFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNTFVSGNCD VVI GIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDLQELGKY EQGS GYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK UniProtKB: Spike glycoprotein, Fibritin |
-Macromolecule #2: Light chain of H18 Fab
Macromolecule | Name: Light chain of H18 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.76852 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGWSCIILFL VATATGVHSA NFMLTQPHSV SESPGKTVTI SCTGSSGSIA SNYVQWYQQR PGSAPTTVIY EDNQRPSGVP DRFSGSIDS SSNSASLTIS GLKTEDEADY YCQSYDSSNV VFGGGTKLTV LGTKLTVLGQ PKAAPSVTLF PPSSEELQAN K ATLVCLIS ...String: MGWSCIILFL VATATGVHSA NFMLTQPHSV SESPGKTVTI SCTGSSGSIA SNYVQWYQQR PGSAPTTVIY EDNQRPSGVP DRFSGSIDS SSNSASLTIS GLKTEDEADY YCQSYDSSNV VFGGGTKLTV LGTKLTVLGQ PKAAPSVTLF PPSSEELQAN K ATLVCLIS DFYPGAVTVA WKADSSPVKA GVETTTPSKQ SNNKYAASSY LSLTPEQWKS HRSYSCQVTH EGSTVEKTVA PT ECS |
-Macromolecule #3: Heavy chain of H18 Fab
Macromolecule | Name: Heavy chain of H18 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.868264 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGWSLILLFL VAVATRVLSQ VQLQESGPGL VKPSETLSLT CTVSGGSVSS GGYFWSWIRQ PPGKGLEWIG CIYYSGSTNY NPSLKSRVT ISVDTSKDQF SLKLSSVTAA DTAVYYCARQ LWLRGRFDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV ...String: MGWSLILLFL VAVATRVLSQ VQLQESGPGL VKPSETLSLT CTVSGGSVSS GGYFWSWIRQ PPGKGLEWIG CIYYSGSTNY NPSLKSRVT ISVDTSKDQF SLKLSSVTAA DTAVYYCARQ LWLRGRFDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PK SCD |
-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: 66 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |