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- EMDB-41842: Prefusion structure of the PRD-0038 spike glycoprotein ectodomain... -

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Basic information

Entry
Database: EMDB / ID: EMD-41842
TitlePrefusion structure of the PRD-0038 spike glycoprotein ectodomain trimer
Map data
Sample
  • Complex: PRD-0038 Spike glycoprotein
    • Protein or peptide: PRD-0038 Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSarbecoviruses / Spike glycoprotein / fusion protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / viral protein
Biological speciesSarbecovirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLee J / Park YJ / Veesler D
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
DepositionSep 5, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41842.png

Downloads & links

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Map

FileDownload / File: emd_41842.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 512 pix.
= 512. Å		1 Å/pix.
x 512 pix.
= 512. Å		1 Å/pix.
x 512 pix.
= 512. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-4.097704 - 6.557691
Average (Standard dev.)0.0018445768 (±0.09642812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 512.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41842_additional_1.map
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Half map: #2

Fileemd_41842_half_map_1.map
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Half map: #1

Fileemd_41842_half_map_2.map
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Sample components

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Entire : PRD-0038 Spike glycoprotein

EntireName: PRD-0038 Spike glycoprotein
Components
  • Complex: PRD-0038 Spike glycoprotein
    • Protein or peptide: PRD-0038 Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PRD-0038 Spike glycoprotein

SupramoleculeName: PRD-0038 Spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sarbecovirus sp.

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Macromolecule #1: PRD-0038 Spike glycoprotein

MacromoleculeName: PRD-0038 Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus sp.
Molecular weightTheoretical: 141.350484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQEGCGILS NKSKPALTQY SSSRRGFYYF DDTFRSSVRV LTTGYFLPFN SNLTGYSSR NAVTGRLIQF DNPNIPFKDG LYFAATERSN VIRGWIFGST LDNTTQSAVL FNNGTHIVIN VCNFYFCQDP M LTVANGSH ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQEGCGILS NKSKPALTQY SSSRRGFYYF DDTFRSSVRV LTTGYFLPFN SNLTGYSSR NAVTGRLIQF DNPNIPFKDG LYFAATERSN VIRGWIFGST LDNTTQSAVL FNNGTHIVIN VCNFYFCQDP M LTVANGSH YKSWVFLNAT NCTYNRVHAF EIDPSLNTGA FIHLREHVFR NVDGFLYVYH NYERANVYDN FPSGFSVLKP IL KLPFGLN ITQFKVIMTL FSPTTSSFNA DASVYFVGHL KPLTMLAEFD ENGTITDAVD CSQDPLSELK CTTKSLTVEK GIY QTSNFR VSPSTEVVRF PNITNLCPFG QVFNASKFPS VYAWERLRIS DCVADYSVLY NSSSSFSTFK CYGVSPTKLN DLCF SSVYA DYFVVKGDDV RQIAPAQTGV IADYNYKLPD DFTGCVLAWN TNSVDSKQGN NFYYRLFRHG KIKPYERDIS NVLYN SAGG TCSSTSQLGC YEPLKSYGFT PTVGVGYQPY RVVVLSFELL NAPATVCGPK KSTELVKNKC VNFNFNGLTG TGVLTS STK KFQPFQQFGR DVSDFTDSVR DPKTLEILDI SPCSYGGVSV ITPGTNTSKA VAVLYQDVNC TDVPTMLHVE QVSTDWR VY ALSADGNMFQ TQAGCLVGAT YENSTYECDI PIGAGICAKF GSNKLRLESI VAYTMSIGED QSIAYSNNTI AIPTNFSI S VTTEVLPVSM TKTSVDCNMY ICGDSTECSN LLLQYGSFCT QLNRALSGIA VEQDRNTRDV FAQTKAIYKT PNIKDFGGF NFSQILPDPK KPSYRSPIED LLYNKVTLSD PGFMKQYGDC LGGINARDLI CAQKFNGLTV LPPLLTDDMI AAYTAALISG TATAGYTFG AGAALQIPFP MQMAYRFNGI GVTQNVLYEN QKQIANQFNN AISKIQDSLT TTPAALGKLQ DVINQNAVAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQAAP HGVVFLHVTY VPSQQQNFTT APAICHNGKA YFPREGVFVM NGTHWFITQR NFYSPQVITT DNT FESGSC DVVIGIVNNT VYDPLQPELE SFKQELDKYF KNHTSPDVDL GDISGINASV VDIKKEIAHL NEIAKNLNES LIDL QELGK YEQYVKSGRE NLYFQGGGGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHHHHGGSS GLNDIFEAQK IEWHE

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 33 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 103347
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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