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- EMDB-25487: SARS-CoV-2 Spike NTD in complex with neutralizing Fab SARS2-57 (l... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | SARS-CoV-2 Spike NTD in complex with neutralizing Fab SARS2-57 (local refinement) | |||||||||
![]() | Local reconstruction of SARS-CoV-2 Spike NTD in complex with Fab SARS2-57 | |||||||||
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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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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: 3.13 Å | |||||||||
![]() | Adams LJ / Fremont DH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A protective antibody targeting the N-terminal domain of SARS-CoV-2 spike recognizes most emerging variants Authors: Adams LJ / VanBlargan LA / Liu Z / Gilchuk P / Zhao H / Chen RE / Raju S / Whitener B / Shrihari S / Jethva PN / Gross ML / Crowe JE / Whelan SPJ / Diamond MS / Fremont DH | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 90.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.4 KB 11.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.4 KB | Display | ![]() |
Images | ![]() | 70.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 347.3 KB | Display | ![]() |
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Full document | ![]() | 346.8 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7swwMC ![]() 7swxC C: citing same article ( M: atomic model generated by this map |
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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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Annotation | Local reconstruction of SARS-CoV-2 Spike NTD in complex with Fab SARS2-57 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : SARS-CoV-2 spike bound by SARS2-57 Fab
Entire | Name: SARS-CoV-2 spike bound by SARS2-57 Fab |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike bound by SARS2-57 Fab
Supramolecule | Name: SARS-CoV-2 spike bound by SARS2-57 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-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: ![]() ![]() |
Molecular weight | Theoretical: 33.082352 KDa |
Recombinant expression | Organism: ![]() |
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 QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLK |
-Macromolecule #2: SARS2-57 Fv heavy chain
Macromolecule | Name: SARS2-57 Fv heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.955321 KDa |
Sequence | String: EVQLQQSGAE LVRPGALVKL SCKASGFNIK DYFVHWVKQR PVQGLEWIGW IDPENGNTIY GPKFQGKASL AADTSSNTGY LQLSSLTSE DTAVYYCARW DGYETLDYWG QGTSVTVS |
-Macromolecule #3: SARS2-57 Fv light chain
Macromolecule | Name: SARS2-57 Fv light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.383759 KDa |
Sequence | String: DIVMSQSPSS LAVSVGEKVT MSCQSSQSLL YSNNEKNYLA WYQQKPGHSP KLLLYWASTR ESGVPDRFTG SGSGTAFTLT ISSVKAEDL AVYYCQQYYN YPYTFGGGTK LEI |
-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: 4 / 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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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |