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- EMDB-41784: PRD-0038 RBD bound to Rhinolophus alcyone ACE2 (local refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-41784
TitlePRD-0038 RBD bound to Rhinolophus alcyone ACE2 (local refinement)
Map data
Sample
  • Complex: PRD-0038 RBD bound to R. alcyone ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: PRD-0038
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsSarbecoviruses / Spike glycoprotein / fusion protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / proteolysis / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesSarbecovirus / Rhinolophus alcyone (Halcyon horseshoe bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPark YJ / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Cell Host Microbe / Year: 2023
Title: Broad receptor tropism and immunogenicity of a clade 3 sarbecovirus.
Authors: Jimin Lee / Samantha K Zepeda / Young-Jun Park / Ashley L Taylor / Joel Quispe / Cameron Stewart / Elizabeth M Leaf / Catherine Treichel / Davide Corti / Neil P King / Tyler N Starr / David Veesler /
Abstract: Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. ...Although Rhinolophus bats harbor diverse clade 3 sarbecoviruses, the structural determinants of receptor tropism along with the antigenicity of their spike (S) glycoproteins remain uncharacterized. Here, we show that the African Rhinolophus bat clade 3 sarbecovirus PRD-0038 S has a broad angiotensin-converting enzyme 2 (ACE2) usage and that receptor-binding domain (RBD) mutations further expand receptor promiscuity and enable human ACE2 utilization. We determine a cryo-EM structure of the PRD-0038 RBD bound to Rhinolophus alcyone ACE2, explaining receptor tropism and highlighting differences with SARS-CoV-1 and SARS-CoV-2. Characterization of PRD-0038 S using cryo-EM and monoclonal antibody reactivity reveals its distinct antigenicity relative to SARS-CoV-2 and identifies PRD-0038 cross-neutralizing antibodies for pandemic preparedness. PRD-0038 S vaccination elicits greater titers of antibodies cross-reacting with vaccine-mismatched clade 2 and clade 1a sarbecoviruses compared with SARS-CoV-2 S due to broader antigenic targeting, motivating the inclusion of clade 3 antigens in next-generation vaccines for enhanced resilience to viral evolution.
History
DepositionAug 29, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41784.png

Downloads & links

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Map

FileDownload / File: emd_41784.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.7006493 - 6.5671473
Average (Standard dev.)0.0008024293 (±0.09430343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41784_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41784_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41784_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PRD-0038 RBD bound to R. alcyone ACE2

EntireName: PRD-0038 RBD bound to R. alcyone ACE2
Components
  • Complex: PRD-0038 RBD bound to R. alcyone ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: PRD-0038
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: PRD-0038 RBD bound to R. alcyone ACE2

SupramoleculeName: PRD-0038 RBD bound to R. alcyone ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sarbecovirus

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus alcyone (Halcyon horseshoe bat)
Molecular weightTheoretical: 89.075398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSSWLFLS LVAVAAAQST PEDLAKIFLD NFNSEAENLS HQSSLASWEY NTNISDENIQ KMDEAGAKWS DFYETQSKHA KNFSLEEIH NDTVKLQLQI LQQSGSPVLS EDKSKRLNSI LNAMSTIYST GKVCRPNNPQ ECLLLEPGLD NIMGTSKDYN E RLWAWEGW ...String:
MSGSSWLFLS LVAVAAAQST PEDLAKIFLD NFNSEAENLS HQSSLASWEY NTNISDENIQ KMDEAGAKWS DFYETQSKHA KNFSLEEIH NDTVKLQLQI LQQSGSPVLS EDKSKRLNSI LNAMSTIYST GKVCRPNNPQ ECLLLEPGLD NIMGTSKDYN E RLWAWEGW RAEVGKQLRP LYEEYVVLKN EMARGYHYED YGDYWRRDYE TEGSPDLEYS RDQLTKDVER IFAEIKPLYE QL HAYVRTK LMDTYPFHIS PTGCLPAHLL GDMWGRFWTN LYPLTVPFAQ KPNIDVTDAM LNQTWDAKRI FKEAEKFFVS IGL PHMTEG FWNNSMLTDP GDGRKVVCHP TAWDLGKGDF RIKMCTKVTM EDFLTAHHEM GHIQYDMAYA SQPYLLRNGA NEGF HEAVG EVMSLSVATP KHLKTMGLLS PDFLEDNETE INFLFKQALT IVGTLPFTYM LEKWRWMVFK GEIPKEEWMT KWWEM KRKI VGVVEPVPHD ETYCDPASLF HVANDYSFIR YYTRTIFEFQ FHEALCRIAK HDGPLHKCDI SNSTDAGKKL HQMLSV GKS QPWTSVLKDF VDSKDMDVGP LLRYFEPLYT WLKEQNRNSF VGWNTDWSPY ADQSIKVRIS LKSALGEKAY EWNNNEM YL FRSSVAYAMR EYFLKTKNQT ILFGEEDVWV SNLKPRISFN FYVTSPRNLS DIIPRPEVEG AIRMSRSRIN DAFRLDDN S LEFLGIQPTL GPPYQPPVTH HHHHHHHGGS SGLNDIFEAQ KIEWHE

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: PRD-0038

MacromoleculeName: PRD-0038 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus
Molecular weightTheoretical: 28.584332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVARF PNITNLCPFG QVFNASKFPS VYAWERLRIS DCVADYSVLY NSSSSFSTFK CYGVSPTKL NDLCFSSVYA DYFVVKGDDV RQIAPAQTGV IADYNYKLPD DFTGCVLAWN TNSVDSKQGN NFYYRLFRHG K IKPYERDI ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVARF PNITNLCPFG QVFNASKFPS VYAWERLRIS DCVADYSVLY NSSSSFSTFK CYGVSPTKL NDLCFSSVYA DYFVVKGDDV RQIAPAQTGV IADYNYKLPD DFTGCVLAWN TNSVDSKQGN NFYYRLFRHG K IKPYERDI SNVLYNSAGG TCSSTSQLGC YEPLKSYGFT PTVGVGYQPY RVVVLSFELL NAPATVCGPK KSTHHHHHHH HG GSSGLND IFEAQKIEWH E

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 284934

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