+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35369 | |||||||||
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Title | Cryo-EM structure of RBD/E77-Fab complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RBD / antibody / complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / symbiont-mediated suppression of host innate immune response / 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 | Mus musculus (house mouse) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Lu DF / Zhang ZC | |||||||||
Funding support | China, 1 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: The structure of the RBD-E77 Fab complex reveals neutralization and immune escape of SARS-CoV-2. Authors: Zhichao Zhang / Xiaoxiong Li / Ying Xue / Bo Yang / Yuanyuan Jia / Shichao Liu / Defen Lu / Abstract: The spike protein (S) of SARS-CoV-2 is the major target of neutralizing antibodies and vaccines. Antibodies that target the receptor-binding domain (RBD) of S have high potency in preventing viral ...The spike protein (S) of SARS-CoV-2 is the major target of neutralizing antibodies and vaccines. Antibodies that target the receptor-binding domain (RBD) of S have high potency in preventing viral infection. The ongoing evolution of SARS-CoV-2, especially mutations occurring in the RBD of new variants, has severely challenged the development of neutralizing antibodies and vaccines. Here, a murine monoclonal antibody (mAb) designated E77 is reported which engages the prototype RBD with high affinity and potently neutralizes SARS-CoV-2 pseudoviruses. However, the capability of E77 to bind RBDs vanishes upon encountering variants of concern (VOCs) which carry the N501Y mutation, such as Alpha, Beta, Gamma and Omicron, in contrast to its performance with the Delta variant. To explain the discrepancy, cryo-electron microscopy was used to analyze the structure of an RBD-E77 Fab complex, which reveals that the binding site of E77 on RBD belongs to the RBD-1 epitope, which largely overlaps with the binding site of human angiotensin-converting enzyme 2 (hACE2). Both the heavy chain and the light chain of E77 interact extensively with RBD and contribute to the strong binding of RBD. E77 employs CDRL1 to engage Asn501 of RBD and the Asn-to-Tyr mutation could generate steric hindrance, abolishing the binding. In sum, the data provide the landscape for an in-depth understanding of immune escape of VOCs and rational antibody engineering against emerging variants of SARS-CoV-2. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35369.map.gz | 78.7 MB | EMDB map data format | |
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Header (meta data) | emd-35369-v30.xml emd-35369.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
Images | emd_35369.png | 40 KB | ||
Others | emd_35369_half_map_1.map.gz emd_35369_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35369 | HTTPS FTP |
-Related structure data
Related structure data | 8idnMC 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_35369.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35369_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35369_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RBD and antibody complex
Entire | Name: RBD and antibody complex |
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Components |
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-Supramolecule #1: RBD and antibody complex
Supramolecule | Name: RBD and antibody complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-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: 23.276104 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ITNLCPFGEV FNATRFATVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF P LQSYGFQP ...String: ITNLCPFGEV FNATRFATVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF P LQSYGFQP TNGVGYQPYR VVVLSFELLH APATVCGPKK STHHHHHH UniProtKB: Spike glycoprotein |
-Macromolecule #2: E77 Fab heavy chain
Macromolecule | Name: E77 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.562865 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVHSQ VQLKESGPGL VAPSQSLSIT CTVSGLSLIG YGVNWVRQPP GKGLEWLGMI WGDGSTDYNS TLKSRLSIS KDNSKSQIFL KMNSLQTIDD ARYYCVRDDD YDGQFAYWGQ GTLVTVSAAK TTPPSVYPLA PGSAAQTNSM V TLGCLVKG ...String: MGWSCIILFL VATATGVHSQ VQLKESGPGL VAPSQSLSIT CTVSGLSLIG YGVNWVRQPP GKGLEWLGMI WGDGSTDYNS TLKSRLSIS KDNSKSQIFL KMNSLQTIDD ARYYCVRDDD YDGQFAYWGQ GTLVTVSAAK TTPPSVYPLA PGSAAQTNSM V TLGCLVKG YFPEPVTVTW NSGSLSSGVH TFPAVLQSDL YTLSSSVTVP SSTWPSETVT CNVAHPASST KVDKKIVPRD C |
-Macromolecule #3: E77 Fab light chain
Macromolecule | Name: E77 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 24.810791 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGWSCIILFL VATATGVHSQ AVVTQESALT TSPGETVTLT CRSSTGAVTI SNYVNWVQEK PDHLFTGLIG ATNSRAPGVP ARFSGSLIG DKAALTITGA QTEDEAIYFC ALWYSNHWVF GGGTKLTVLG QPKSTPSLTV FPPSSEELKE NKATLVCLIS N FSPSGVTV ...String: MGWSCIILFL VATATGVHSQ AVVTQESALT TSPGETVTLT CRSSTGAVTI SNYVNWVQEK PDHLFTGLIG ATNSRAPGVP ARFSGSLIG DKAALTITGA QTEDEAIYFC ALWYSNHWVF GGGTKLTVLG QPKSTPSLTV FPPSSEELKE NKATLVCLIS N FSPSGVTV AWKANGTPIT QGVDTSNPTK EGNKFMASSF LHLTSDQWRS HNSFTCQVTH EGDTVEKSLS PAECL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: C-flat / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201353 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |