+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23717 | |||||||||
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Title | SARS-CoV-2 S-NTD + Fab CM25 | |||||||||
Map data | Focused map, calculated in cryoSPARC. | |||||||||
Sample |
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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 | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Johnson NV / Mclellan JS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2021 Title: Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Authors: William N Voss / Yixuan J Hou / Nicole V Johnson / George Delidakis / Jin Eyun Kim / Kamyab Javanmardi / Andrew P Horton / Foteini Bartzoka / Chelsea J Paresi / Yuri Tanno / Chia-Wei Chou / ...Authors: William N Voss / Yixuan J Hou / Nicole V Johnson / George Delidakis / Jin Eyun Kim / Kamyab Javanmardi / Andrew P Horton / Foteini Bartzoka / Chelsea J Paresi / Yuri Tanno / Chia-Wei Chou / Shawn A Abbasi / Whitney Pickens / Katia George / Daniel R Boutz / Dalton M Towers / Jonathan R McDaniel / Daniel Billick / Jule Goike / Lori Rowe / Dhwani Batra / Jan Pohl / Justin Lee / Shivaprakash Gangappa / Suryaprakash Sambhara / Michelle Gadush / Nianshuang Wang / Maria D Person / Brent L Iverson / Jimmy D Gollihar / John M Dye / Andrew S Herbert / Ilya J Finkelstein / Ralph S Baric / Jason S McLellan / George Georgiou / Jason J Lavinder / Gregory C Ippolito / Abstract: The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are ...The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23717.map.gz | 290.4 MB | EMDB map data format | |
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Header (meta data) | emd-23717-v30.xml emd-23717.xml | 23.1 KB 23.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23717_fsc.xml | 16.3 KB | Display | FSC data file |
Images | emd_23717.png | 72.1 KB | ||
Others | emd_23717_additional_1.map.gz emd_23717_additional_2.map.gz emd_23717_half_map_1.map.gz emd_23717_half_map_2.map.gz | 290.2 MB 193.1 MB 285.2 MB 285.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23717 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23717 | HTTPS FTP |
-Validation report
Summary document | emd_23717_validation.pdf.gz | 659.3 KB | Display | EMDB validaton report |
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Full document | emd_23717_full_validation.pdf.gz | 658.8 KB | Display | |
Data in XML | emd_23717_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | emd_23717_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23717 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23717 | HTTPS FTP |
-Related structure data
Related structure data | 7m8jMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23717.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Focused map, calculated in cryoSPARC. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Full map used for focused refinement. Calculated and...
File | emd_23717_additional_1.map | ||||||||||||
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Annotation | Full map used for focused refinement. Calculated and sharpened in cryoSPARC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused map, calculated in cryoSPARC and sharpened in deepEMhancer.
File | emd_23717_additional_2.map | ||||||||||||
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Annotation | Focused map, calculated in cryoSPARC and sharpened in deepEMhancer. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_23717_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_23717_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of SARS-CoV-2 S-ECD with CM25 Fab
Entire | Name: Complex of SARS-CoV-2 S-ECD with CM25 Fab |
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Components |
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-Supramolecule #1: Complex of SARS-CoV-2 S-ECD with CM25 Fab
Supramolecule | Name: Complex of SARS-CoV-2 S-ECD with CM25 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | 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 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 29.297074 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GD SSSGWTA GAAAYYVGYL |
-Macromolecule #2: CM25 Fab - Heavy Chain
Macromolecule | Name: CM25 Fab - 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: 13.091598 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VQLVQSGAEV KKPGASVKVS CKVSGYTLTE LSMHWVRQAP GKGLEWMGGF DPEDGETIYA QKFQGRVTMT EDTSTDTAYM ELSSLRSED TAVYYCATGP AVRRGSWFDP WGQGTLVTVS S |
-Macromolecule #3: CM25 Fab - Light Chain
Macromolecule | Name: CM25 Fab - 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: 11.381535 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VVTQPPSVSA APGQKVTISC SGSSSNIGNN YVSWYQQLPG TAPKLLIYDN NKRPSGIPDR FSGSKSGTSA TLGITGLQTG DEADYYCGT WDSSLSAHWV FGGGTKLTVL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: -4 force, 3 s blot. | |||||||||
Details | Sample was monodisperse. All S proteins had 3 Fabs bound. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |