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Yorodumi- EMDB-13667: Structure of the membrane soluble spike complex from the Lassa vi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13667 | |||||||||
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Title | Structure of the membrane soluble spike complex from the Lassa virus in a C1-symmetric map focused on the ectodomain | |||||||||
Map data | 3.7A low-pass filtered C1-symmetric map | |||||||||
Sample |
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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 / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Lassa virus Josiah / Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Diskin R / Katz M | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13667.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-13667-v30.xml emd-13667.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13667_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_13667.png | 121.4 KB | ||
Masks | emd_13667_msk_1.map | 64 MB | Mask map | |
Others | emd_13667_additional_1.map.gz emd_13667_half_map_1.map.gz emd_13667_half_map_2.map.gz | 32.3 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13667 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13667 | HTTPS FTP |
-Validation report
Summary document | emd_13667_validation.pdf.gz | 596.4 KB | Display | EMDB validaton report |
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Full document | emd_13667_full_validation.pdf.gz | 596 KB | Display | |
Data in XML | emd_13667_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_13667_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13667 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13667 | HTTPS FTP |
-Related structure data
Related structure data | 7pvdMC 7puyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13667.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3.7A low-pass filtered C1-symmetric map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.038 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13667_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered C1-symmetric map
File | emd_13667_additional_1.map | ||||||||||||
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Annotation | Unfiltered C1-symmetric map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_13667_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_13667_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The complete spike complex
Entire | Name: The complete spike complex |
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Components |
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-Supramolecule #1: The complete spike complex
Supramolecule | Name: The complete spike complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Lassa virus Josiah |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Glycoprotein G2
Macromolecule | Name: Glycoprotein G2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) Strain: Mouse/Sierra Leone/Josiah/1976 |
Molecular weight | Theoretical: 28.083273 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAE AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGKTP ...String: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAE AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGKTP LGLVDLFVFS TSFYLISIFL HLVKIPTHRH IVGKSCPKPH RLNHMGICSC GLYKQPGVPV KWKRGGGSDY KD DDDK |
-Macromolecule #2: Pre-glycoprotein polyprotein GP complex
Macromolecule | Name: Pre-glycoprotein polyprotein GP complex / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) Strain: Mouse/Sierra Leone/Josiah/1976 |
Molecular weight | Theoretical: 29.064402 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL ...String: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL SHSYAGDAAN HCGTVANGVL QTFMRMAWGG SYIALDSGRG NWDCIMTSYQ YLIIQNTTWE DHCQFSRPSP IG YLGLLSQ RTRDIYISRR LL |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 73.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |