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Yorodumi- EMDB-50503: Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50503 | |||||||||
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Title | Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 | |||||||||
Map data | Globally refined map - spike trimer fab | |||||||||
Sample |
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Keywords | Neutralizing Antibody / Conserved Epitope / Covid-19 / Spike / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information virion component / 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 ...virion component / 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 / 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 | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Enterobacteria phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Bjoernsson KH / Walker MR / Raghavan SSR / Ward AB / Barfod LK | |||||||||
Funding support | Denmark, 1 items
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Citation | Journal: To Be Published Title: Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 Authors: Bjoernsson KH / Walker MR / Raghavan SSR / Ward AB / Barfod LK | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50503.map.gz | 483.9 MB | EMDB map data format | |
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Header (meta data) | emd-50503-v30.xml emd-50503.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50503_fsc.xml | 23.5 KB | Display | FSC data file |
Images | emd_50503.png | 99.7 KB | ||
Filedesc metadata | emd-50503.cif.gz | 6.9 KB | ||
Others | emd_50503_additional_1.map.gz emd_50503_half_map_1.map.gz emd_50503_half_map_2.map.gz | 483.8 MB 474.6 MB 474.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50503 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50503 | HTTPS FTP |
-Validation report
Summary document | emd_50503_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_50503_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_50503_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | emd_50503_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50503 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50503 | HTTPS FTP |
-Related structure data
Related structure data | 9fjkMC 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_50503.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Globally refined map - spike trimer fab | ||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Alphacoronavirus
Entire | Name: Alphacoronavirus |
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Components |
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-Supramolecule #1: Alphacoronavirus
Supramolecule | Name: Alphacoronavirus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Omicron BA.1 spike trimer with Fab fragment of human monoclonal antibody K501SP6 produced with hybridoma technology |
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-Supramolecule #2: Antibody
Supramolecule | Name: Antibody / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3 / Details: Human monoclonal antibody |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Spike glycoprotein with fibritin
Supramolecule | Name: Spike glycoprotein with fibritin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 / Details: Omicron BA.1 spike trimer |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron BA.1 |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterobacteria phage T4 (virus) |
Molecular weight | Theoretical: 141.481031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DHKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPILVR EPEDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NLAPFFTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYSF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLK GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFKGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIF SRLDPPEAEV 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 GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GSAWSHPQFE KGGGSGGGGS GGSAWSHPQF EK UniProtKB: Spike glycoprotein, Fibritin |
-Macromolecule #2: K501SP6 Fv Heavy Chain
Macromolecule | Name: K501SP6 Fv Heavy Chain / 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: 14.387906 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQESGPG LVKPSETLSL TCTVSGGSIS SRSYYWGWIR QPPGKGLEWI GSIYYSGSTY YNPSLKSRVT ISVDTSKNQF SLKMNSMTA ADTAVYYCAR LRGDEIYYES SGYYSYFDYW GQGTLVTVSS |
-Macromolecule #3: K501SP6 Fv Light Chain
Macromolecule | Name: K501SP6 Fv Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.002314 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: WAQSALTQPP SVSGAPGQRV AISCTGSSAN IGTADDVHWY QQLPRTAPKL LIYGNNNRPS GVPDRFSGSQ SGTSASLVIT GLQPEDEAD YFCQSYDSSL SGYVFGTGTK VTVLGQPKAA PSVTLFPPSS EELQA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 7.5 / Details: TBS, pH 7.5 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 195000 |
Sample stage | Cooling holder cryogen: NITROGEN |