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- EMDB-41843: PRD-0038 Spike glycoprotein NTD -

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Basic information

Entry
Database: EMDB / ID: EMD-41843
TitlePRD-0038 Spike glycoprotein NTD
Map data
Sample
  • Complex: PRD-0038 Spike glycoprotein
    • Protein or peptide: PRD-0038 Spike glycoprotein NTD
KeywordsSarbecoviruses / Spike glycoprotein / fusion protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / viral protein
Biological speciesSarbecovirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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: Lee J / Zepeda SK / Park YJ / Taylor AL / Quispe J / Stewart C / Leaf EM / Treichel C / Corti D / King NP / Starr TN / Veesler D
History
DepositionSep 5, 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

Downloads & links

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Map

FileDownload / File: emd_41843.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-6.1685643 - 11.317902999999999
Average (Standard dev.)0.0018123615 (±0.08403696)
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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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 NTD

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Supramolecule #1: PRD-0038 Spike glycoprotein

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

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Macromolecule #1: PRD-0038 Spike glycoprotein NTD

MacromoleculeName: PRD-0038 Spike glycoprotein NTD / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus sp.
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQEGCGILS NKSKPALTQY SSSRRGFYYF DDTFRSSVRV LTTGYFLPFN SNLTGYSSRN AVTGRLIQFD NPNIPFKDGL YFAATERSNV IRGWIFGSTL DNTTQSAVLF NNGTHIVINV CNFYFCQDPM LTVANGSHYK ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQEGCGILS NKSKPALTQY SSSRRGFYYF DDTFRSSVRV LTTGYFLPFN SNLTGYSSRN AVTGRLIQFD NPNIPFKDGL YFAATERSNV IRGWIFGSTL DNTTQSAVLF NNGTHIVINV CNFYFCQDPM LTVANGSHYK SWVFLNATNC TYNRVHAFEI DPSLNTGAFI HLREHVFRNV DGFLYVYHNY ERANVYDNFP SGFSVLKPIL KLPFGLNITQ FKVIMTLFSP TTSSFNADAS VYFVGHLKPL TMLAEFDENG TITDAVDCSQ DPLSELKCTT KSLTVEKGIY QTSNFRVSPS TEVVRFPNIT NLCPFGQVFN ASKFPSVYAW ERLRISDCVA DYSVLYNSSS SFSTFKCYGV SPTKLNDLCF SSVYADYFVV KGDDVRQIAP AQTGVIADYN YKLPDDFTGC VLAWNTNSVD SKQGNNFYYR LFRHGKIKPY ERDISNVLYN SAGGTCSSTS QLGCYEPLKS YGFTPTVGVG YQPYRVVVLS FELLNAPATV CGPKKSTELV KNKCVNFNFN GLTGTGVLTS STKKFQPFQQ FGRDVSDFTD SVRDPKTLEI LDISPCSYGG VSVITPGTNT SKAVAVLYQD VNCTDVPTML HVEQVSTDWR VYALSADGNM FQTQAGCLVG ATYENSTYEC DIPIGAGICA KFGSNKLRLE SIVAYTMSIG EDQSIAYSNN TIAIPTNFSI SVTTEVLPVS MTKTSVDCNM YICGDSTECS NLLLQYGSFC TQLNRALSGI AVEQDRNTRD VFAQTKAIYK TPNIKDFGGF NFSQILPDPK KPSYRSPIED LLYNKVTLSD PGFMKQYGDC LGGINARDLI CAQKFNGLTV LPPLLTDDMI AAYTAALISG TATAGYTFGA GAALQIPFPM QMAYRFNGIG VTQNVLYENQ KQIANQFNNA ISKIQDSLTT TPAALGKLQD VINQNAVALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQAAPHGV VFLHVTYVPS QQQNFTTAPA ICHNGKAYFP REGVFVMNGT HWFITQRNFY SPQVITTDNT FESGSCDVVI GIVNNTVYDP LQPELESFKQ ELDKYFKNHT SPDVDLGDIS GINASVVDIK KEIAHLNEIA KNLNESLIDL QELGKYEQYV KSGRENLYFQ GGGGSGYIPE APRDGQAYVR KDGEWVLLST FLGHHHHHHH HGGSSGLNDI FEAQKIEWHE

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 310041
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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