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- EMDB-46955: Designed miniproteins potently inhibit and protect against MERS_C... -

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Basic information

Entry
Database: EMDB / ID: EMD-46955
TitleDesigned miniproteins potently inhibit and protect against MERS_CoV. MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global refinement.
Map dataMain map
Sample
  • Complex: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global refinement.
    • Protein or peptide: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7
KeywordsCoronavirus / betacoronavirus / MERS-CoV / single particle cryo-EM / neutralization assays / binding assays / miniproteins inhibitors / fusion assays / in vivo protection / VIRAL PROTEIN
Biological speciesMiddle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTortorici MA / 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: To Be Published
Title: Designed miniproteins potently inhibit and protect against MERS_CoV. MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global refinement.
Authors: Tortorici MA / Veesler D
History
DepositionSep 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46955.png

Downloads & links

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Map

FileDownload / File: emd_46955.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-3.8447094 - 5.9583
Average (Standard dev.)-0.00015415979 (±0.06286478)
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: Unsharpened map

Fileemd_46955_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_46955_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_46955_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global r...

EntireName: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global refinement.
Components
  • Complex: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global refinement.
    • Protein or peptide: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7

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Supramolecule #1: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global r...

SupramoleculeName: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7. Global refinement.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

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Macromolecule #1: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7

MacromoleculeName: MERS_CoV S in complex with cb3_GGGSGGGS_SB175, linker 7
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTVDVGPDSV KSACIEVDIQ QTFFDKTWPR PIDVSKADGI IYPQGRTYSN ITITYQGLFP YQGDHGDMYV YSAGHATGTT PQKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTVDVGPDSV KSACIEVDIQ QTFFDKTWPR PIDVSKADGI IYPQGRTYSN ITITYQGLFP YQGDHGDMYV YSAGHATGTT PQKLFVANYS QDVKQFANGF VVRIGAAANS TGTVIISPST SATIRKIYPA FMLGSSVGNF SDGKMGRFFN HTLVLLPDGC GTLLRAFYCI LEPRSGNHCP AGNSYTSFAT YHTPATDCSD GNYNRNASLN SFKEYFNLRN CTFMYTYNIT EDEILEWFGI TQTAQGVHLF SSRYVDLYGG NMFQFATLPV YDTIKYYSII PHSIRSIQSD RKAWAAFYVY KLQPLTFLLD FSVDGYIRRA IDCGFNDLSQ LHCSYESFDV ESGVYSVSSF EAKPSGSVVE QAEGVECDFS PLLSGTPPQV YNFKRLVFTN CNYNLTKLLS LFSVNDFTCS QISPAAIASN CYSSLILDYF SYPLSMKSDL SVSSAGPISQ FNYKQSFSNP TCLILATVPH NLTTITKPLK YSYINKCSRL LSDDRTEVPQ LVNANQYSPC VSIVPSTVWE DGDYYRKQLS PLEGGGWLVA SGSTVAMTEQ LQMGFGITVQ YGTDTNSVCP KLEFANDTKI ASQLGNCVEY SLYGVSGRGV FQNCTAVGVR QQRFVYDAYQ NLVGYYSDDG NYYCLRACVS VPVSVIYDKE TKTHATLFGS VACEHISSTM SQYSRSTRSM LKRRDSTYGP LQTPVGCVLG LVNSSLFVED CKLPLGQSLC ALPDTPSTLT PASVGSVPGE MRLASIAFNH PIQVDQLNSS YFKLSIPTNF SFGVTQEYIQ TTIQKVTVDC KQYVCNGFQK CEQLLREYGQ FCSKINQALH GANLRQDDSV RNLFASVKSS QSSPIIPGFG GDFNLTLLEP VSISTGSRSA RSAIEDLLFD KVTIADPGYM QGYDDCMQQG PASARDLICA QYVAGYKVLP PLMDVNMEAA YTSSLLGSIA GVGWTAGLSS FAAIPFAQSI FYRLNGVGIT QQVLSENQKL IANKFNQALG AMQTGFTTTN EAFQKVQDAV NNNAQALSKL ASELSNTFGA ISASIGDIIQ RLDPPEQDAQ IDRLINGRLT TLNAFVAQQL VRSESAALSA QLAKDKVNEC VKAQSKRSGF CGQGTHIVSF VVNAPNGLYF MHVGYYPSNH IEVVSAYGLC DAANPTNCIA PVNGYFIKTN NTRIVDEWSY TGSSFYAPEP ITSLNTKYVA PQVTYQNIST NLPPPLLGNS TGIDFQDELD EFFKNVSTSI PNFGSLTQIN TTLLDLTYEM LSLQQVVKAL NESYIDLKEL GNYTYYNKGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGGS GLNDIFEAQK IEWHEGGSHH HHHHHH

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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: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538654
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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