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- EMDB-13668: C3-focused map on the ectodomain of the Lassa virus spike complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13668
TitleC3-focused map on the ectodomain of the Lassa virus spike complex
Map dataC3-symmetric focused map
Sample
  • Complex: The complete spike complex
    • Protein or peptide: Membrane-soluble trimeric spike complex from the Lassa virus
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa virus Josiah
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsDiskin R / Katz M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Structure and receptor recognition by the Lassa virus spike complex.
Authors: Michael Katz / Jonathan Weinstein / Maayan Eilon-Ashkenazy / Katrin Gehring / Hadas Cohen-Dvashi / Nadav Elad / Sarel J Fleishman / Ron Diskin /
Abstract: Lassa virus (LASV) is a human pathogen, causing substantial morbidity and mortality. Similar to other Arenaviridae, it presents a class-I spike complex on its surface that facilitates cell entry. The ...Lassa virus (LASV) is a human pathogen, causing substantial morbidity and mortality. Similar to other Arenaviridae, it presents a class-I spike complex on its surface that facilitates cell entry. The virus's cellular receptor is matriglycan, a linear carbohydrate that is present on α-dystroglycan, but the molecular mechanism that LASV uses to recognize this glycan is unknown. In addition, LASV and other arenaviruses have a unique signal peptide that forms an integral and functionally important part of the mature spike; yet the structure, function and topology of the signal peptide in the membrane remain uncertain. Here we solve the structure of a complete native LASV spike complex, finding that the signal peptide crosses the membrane once and that its amino terminus is located in the extracellular region. Together with a double-sided domain-switching mechanism, the signal peptide helps to stabilize the spike complex in its native conformation. This structure reveals that the LASV spike complex is preloaded with matriglycan, suggesting the mechanism of binding and rationalizing receptor recognition by α-dystroglycan-tropic arenaviruses. This discovery further informs us about the mechanism of viral egress and may facilitate the rational design of novel therapeutics that exploit this binding site.
History
DepositionOct 2, 2021-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13668.png

Downloads & links

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Map

FileDownload / File: emd_13668.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3-symmetric focused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 265.728 Å		1.04 Å/pix.
x 256 pix.
= 265.728 Å		1.04 Å/pix.
x 256 pix.
= 265.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.038 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.3757513 - 0.86063963
Average (Standard dev.)-0.0014186188 (±0.01702854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 265.728 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0381.0381.038
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z265.728265.728265.728
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3760.861-0.001

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Supplemental data

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Mask #1

Fileemd_13668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_13668_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_13668_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complete spike complex

EntireName: The complete spike complex
Components
  • Complex: The complete spike complex
    • Protein or peptide: Membrane-soluble trimeric spike complex from the Lassa virus

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Supramolecule #1: The complete spike complex

SupramoleculeName: The complete spike complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lassa virus Josiah
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Membrane-soluble trimeric spike complex from the Lassa virus

MacromoleculeName: Membrane-soluble trimeric spike complex from the Lassa virus
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQ TLELNMETLN MTMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN L SDAHKKNL YDHALMSIIS TFHLSIPNFN QYEAMSCDFN GGKISVQYNL ...String:
MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQ TLELNMETLN MTMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN L SDAHKKNL YDHALMSIIS TFHLSIPNFN QYEAMSCDFN GGKISVQYNL SHSYAGDAAN HC GTVANGV LQTFMRMAWG GSYIALDSGR GNWDCIMTSY QYLIIQNTTW EDHCQFSRPS PIG YLGLLS QRTRDIYISR RLLGTFTWTL SDSEGKDTPG GYCLTRWMLI EAELKCFGNT AVAK CNEKH DEEFCDMLRL FDFNKQAIQR LKAEAQMSIQ LINKAVNALI NDQLIMKNHL RDIMG IPYC NYSKYWYLNH TTTGRTSLPK CWLVSNGSYL NETHFSDDIE QQADNMITEM LQKEYM ERQ GKTPLGLVDL FVFSTSFYLI SIFLHLVKIP THRHIVGKSC PKPHRLNHMG ICSCGLY KQ PGVPVKWKRG GGSDYKDDDD K

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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: 7.4
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: 73.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Focused reconstruction on the ectodomain of the spike
Number images used: 221927
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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