[English] 日本語
Yorodumi- EMDB-28537: cryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28537 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | cryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibody STI-9167 | |||||||||
Map data | deepEMhancer sharpened focused map | |||||||||
Sample |
| |||||||||
Keywords | antibody / SARS-CoV-2 / IMMUNE SYSTEM | |||||||||
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 | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Bajic G | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: mBio / Year: 2024 Title: An experimental pipeline to characterize the epitope of a SARS-CoV-2 neutralizing antibody. Authors: Kristina E Atanasoff / Luca Brambilla / Daniel C Adelsberg / Shreyas Kowdle / Christian S Stevens / Stefan Slamanig / Chuan-Tien Hung / Yanwen Fu / Reyna Lim / Linh Tran / Robert Allen / ...Authors: Kristina E Atanasoff / Luca Brambilla / Daniel C Adelsberg / Shreyas Kowdle / Christian S Stevens / Stefan Slamanig / Chuan-Tien Hung / Yanwen Fu / Reyna Lim / Linh Tran / Robert Allen / Weina Sun / J Andrew Duty / Goran Bajic / Benhur Lee / Domenico Tortorella / Abstract: The COVID-19 pandemic remains a significant public health concern for the global population; the development and characterization of therapeutics, especially ones that are broadly effective, will ...The COVID-19 pandemic remains a significant public health concern for the global population; the development and characterization of therapeutics, especially ones that are broadly effective, will continue to be essential as severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants emerge. Neutralizing monoclonal antibodies remain an effective therapeutic strategy to prevent virus infection and spread so long as they recognize and interact with circulating variants. The epitope and binding specificity of a neutralizing anti-SARS-CoV-2 Spike receptor-binding domain antibody clone against many SARS-CoV-2 variants of concern were characterized by generating antibody-resistant virions coupled with cryo-EM structural analysis and VSV-spike neutralization studies. This workflow can serve to predict the efficacy of antibody therapeutics against emerging variants and inform the design of therapeutics and vaccines. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28537.map.gz | 448.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28537-v30.xml emd-28537.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28537_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_28537.png | 62 KB | ||
Filedesc metadata | emd-28537.cif.gz | 6.1 KB | ||
Others | emd_28537_additional_1.map.gz emd_28537_half_map_1.map.gz emd_28537_half_map_2.map.gz | 483.2 MB 474.4 MB 474.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28537 | HTTPS FTP |
-Validation report
Summary document | emd_28537_validation.pdf.gz | 770.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28537_full_validation.pdf.gz | 770.2 KB | Display | |
Data in XML | emd_28537_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | emd_28537_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28537 | HTTPS FTP |
-Related structure data
Related structure data | 8eqfMC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
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_28537.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | deepEMhancer sharpened focused map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: #1
File | emd_28537_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_28537_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_28537_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike RBD in complex with 10A3 Fab
Entire | Name: SARS-CoV-2 spike RBD in complex with 10A3 Fab |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 spike RBD in complex with 10A3 Fab
Supramolecule | Name: SARS-CoV-2 spike RBD in complex with 10A3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 21.776381 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCG UniProtKB: Spike glycoprotein |
-Macromolecule #2: Fab heavy chain
Macromolecule | Name: Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.956542 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGMNWVRQA PGKGLEWVAI IWYDGNNKYY VDSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARK DYSKTYYGYY FDYWGQGTLV TVSS |
-Macromolecule #3: Fab light chain
Macromolecule | Name: Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.6199 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSIH SFLNWYQQKP GKPPNLLIYA ASSLQSGLPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYITPPTFG HGTKVEIK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.92 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |