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Yorodumi- EMDB-25797: Locally refined region of SARS-CoV-2 spike in complex with antibo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25797 | |||||||||
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Title | Locally refined region of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 | |||||||||
Map data | Locally refined cryo-EM map of SARS-CoV-2 RBD in complex with antibody B1-182.1 and A19-61.1 FV regions, needs to be z-flipped for refinement. | |||||||||
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 / 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 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Zhou T / Tsybovsky T / Kwong PD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2022 Title: Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng ...Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng / Adrian Creanga / Claudia Jenkins / Kwanyee Leung / Tracy Liu / Erik-Stephane D Stancofski / Tyler Stephens / Baoshan Zhang / Yaroslav Tsybovsky / Barney S Graham / John R Mascola / Nancy J Sullivan / Peter D Kwong / Abstract: The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a ...The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25797.map.gz | 267.6 MB | EMDB map data format | |
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Header (meta data) | emd-25797-v30.xml emd-25797.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
Images | emd_25797.png | 50 KB | ||
Masks | emd_25797_msk_1.map | 536.4 MB | Mask map | |
Others | emd_25797_additional_1.map.gz emd_25797_half_map_1.map.gz emd_25797_half_map_2.map.gz | 506.2 MB 497.5 MB 497.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25797 | HTTPS FTP |
-Validation report
Summary document | emd_25797_validation.pdf.gz | 901.3 KB | Display | EMDB validaton report |
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Full document | emd_25797_full_validation.pdf.gz | 900.8 KB | Display | |
Data in XML | emd_25797_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_25797_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25797 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25797 | HTTPS FTP |
-Related structure data
Related structure data | 7tbfMC 7tb8C 7tc9C 7tcaC 7tccC 7u0dC 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_25797.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Locally refined cryo-EM map of SARS-CoV-2 RBD in complex with antibody B1-182.1 and A19-61.1 FV regions, needs to be z-flipped for refinement. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.873 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25797_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally refined and sharpened cryo-EM map of SARS-CoV-2...
File | emd_25797_additional_1.map | ||||||||||||
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Annotation | Locally refined and sharpened cryo-EM map of SARS-CoV-2 RBD in complex with antibody B1-182.1 and A19-61.1 FV regions | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of SARS-CoV-2 RBD in complex...
File | emd_25797_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map of SARS-CoV-2 RBD in complex with antibody B1-182.1 and A19-61.1 FV regions. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of SARS-CoV-2 RBD in complex...
File | emd_25797_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map of SARS-CoV-2 RBD in complex with antibody B1-182.1 and A19-61.1 FV regions. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1
Entire | Name: SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1
Supramolecule | Name: SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / 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: 21.986652 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ITNLCPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF P LQSYGFQP ...String: ITNLCPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF P LQSYGFQP TNGVGYQPYR VVVLSFELLH APATVCGP |
-Macromolecule #2: Heavy chain of SARS-CoV-2 antibody B1-182.1
Macromolecule | Name: Heavy chain of SARS-CoV-2 antibody B1-182.1 / 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: 24.285312 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFT SSAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQKFQERVTI TRDMSTSTAY MELSSLRSE DTAVYYCAAP YCSGGSCFDG FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFT SSAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQKFQERVTI TRDMSTSTAY MELSSLRSE DTAVYYCAAP YCSGGSCFDG FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK |
-Macromolecule #3: Light chain of SARS-CoV-2 antibody B1-182.1
Macromolecule | Name: Light chain of SARS-CoV-2 antibody B1-182.1 / 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: 23.536008 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGFP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGNSPWTF GQGTKVEIRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGFP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGNSPWTF GQGTKVEIRR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: Heavy chain of SARS-CoV-2 antibody A19-61.1
Macromolecule | Name: Heavy chain of SARS-CoV-2 antibody A19-61.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.934431 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYAFHWVRQA PGKGLEWVAV ISYDGSNQYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAD DTAVYYCARD LAIAVAGTWH YYNGMDVWGQ GTTVTVSS |
-Macromolecule #5: Light chain of SARS-CoV-2 antibody A19-61.1
Macromolecule | Name: Light chain of SARS-CoV-2 antibody A19-61.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.571899 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS VSASVGDRVI ITCRASQGIS SWLAWYQQKP GKAPKVLIYD ASSLQSGVPS RFSGSGYGTD FTLTISSLQP EDSATYYCQ QAKSFPITFG QGTRLEIK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 / Details: 100 mM HEPES, 150 mM NaCl |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2-3.5 seconds before plugging.. |
Details | Complex at 0.5 mg/mL concentration in the buffer |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: OTHER / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |