+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16397 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Antibody / Spike / Complex / VIRAL PROTEIN | |||||||||
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 / 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 | Severe acute respiratory syndrome coronavirus 2 / Enterobacteria phage T4 (virus) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
Authors | Das H / Hallberg BM | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: To Be Published Title: SARS-CoV-2 omicron Spike (RBD) in complex with CAB-A17 antibody Authors: Das H / Hallberg BM | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_16397.map.gz | 190.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-16397-v30.xml emd-16397.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16397_fsc.xml | 19.7 KB | Display | FSC data file |
Images | emd_16397.png | 105.3 KB | ||
Filedesc metadata | emd-16397.cif.gz | 7 KB | ||
Others | emd_16397_additional_1.map.gz emd_16397_half_map_1.map.gz emd_16397_half_map_2.map.gz | 223.1 MB 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16397 | HTTPS FTP |
-Validation report
Summary document | emd_16397_validation.pdf.gz | 671.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_16397_full_validation.pdf.gz | 671.1 KB | Display | |
Data in XML | emd_16397_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | emd_16397_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16397 | HTTPS FTP |
-Related structure data
Related structure data | 8c2rMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_16397.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: raw map
File | emd_16397_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | raw map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: halfmap B
File | emd_16397_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | halfmap B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: halfmap A
File | emd_16397_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | halfmap A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
Entire | Name: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
Supramolecule | Name: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Molecular weight | Theoretical: 95.7 KDa |
-Supramolecule #2: SARS-CoV2 Omicron BA.1 spike
Supramolecule | Name: SARS-CoV2 Omicron BA.1 spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: CAB-A17 Antibody (FAB)
Supramolecule | Name: CAB-A17 Antibody (FAB) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
---|---|
Source (natural) | Organism: Enterobacteria phage T4 (virus) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 124.773758 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVIHVSGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGWI FGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLREFV ...String: PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVIHVSGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGWI FGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG N FKNLREFV FKNIDGYFKI YSKHTPINLV RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AY YVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNLCPFDEVF NAT RFASVY AWNRKRISNC VADYSVLYNL APFFTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGNIADY NYKL PDDFT GCVIAWNSNK LDSKVSGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC NGVAGFNCYF PLRSYSFRPT YGVGH QPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLKGT GVLTESNKKF LPFQQFGRDI ADTTDAVRDP QTLEIL DIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEYVNN SYECDIP IG AGICASYQTQ TNSPRRARSV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTSVD CTMYICGD S TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKY FGGFNFSQIL PDPSKPSKRS PIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF KGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNH NAQALNTLVK QLSSKFGAIS SVLNDIFSRL D PPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HV TYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNNTVYDPLQ PEL DS UniProtKB: Spike glycoprotein |
-Macromolecule #2: CAB-A17 antibody (LC)
Macromolecule | Name: CAB-A17 antibody (LC) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.284832 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAS LSCRASQSLS TYLAWYQQKP GQAPRLLIFG ASSRASGIPD RFSGGGSGTD FTLTISRLEP EDFAVYYCQ QYGSSPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: EIVLTQSPGT LSLSPGERAS LSCRASQSLS TYLAWYQQKP GQAPRLLIFG ASSRASGIPD RFSGGGSGTD FTLTISRLEP EDFAVYYCQ QYGSSPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #3: CAB-A17 antibody (HC)
Macromolecule | Name: CAB-A17 antibody (HC) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.900543 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DVHLVESGGG LIQPGGSLRL SCAASEFIVS ANYMSWVRQA PGEGLQWVSV IYPGGSTFYA ESVKGRFTIS RDNSRNTLYL QMNSLRAED TGVYYCARDY GDFYFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSTAALGCL VKDYFPEPVT VSWNSGALTS G VHTFPAVL ...String: DVHLVESGGG LIQPGGSLRL SCAASEFIVS ANYMSWVRQA PGEGLQWVSV IYPGGSTFYA ESVKGRFTIS RDNSRNTLYL QMNSLRAED TGVYYCARDY GDFYFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSTAALGCL VKDYFPEPVT VSWNSGALTS G VHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKS |
-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: 22 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
---|---|
Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 25652 / Average exposure time: 1.5 sec. / Average electron dose: 54.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |