+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17428 | |||||||||
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Title | The spike complex of the Lujo Virus | |||||||||
Map data | Unfiltered map | |||||||||
Sample |
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Keywords | Spike complex / VIRAL PROTEIN | |||||||||
Function / homology | Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / host cell Golgi apparatus / viral envelope / membrane / Glycoprotein Function and homology information | |||||||||
Biological species | Lujo mammarenavirus / Mammarenavirus lujoense | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Eilon-Ashkenazy M / Diskin R | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: The structure of the Lujo virus spike complex. Authors: Maayan Eilon-Ashkenazy / Hadas Cohen-Dvashi / Sarah Borni / Ron Shaked / Rivka Calinsky / Yaakov Levy / Ron Diskin / Abstract: Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old ...Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old World" and "New World" serogroups, but it uses a cell-entry receptor, neuropilin-2 (NRP2), that is distinct from the receptors of OW and NW viruses. Though the receptor binding domain of LUJV has been characterized structurally, the overall organization of the trimeric spike complex and how NRP2 is recognized in this context were unknown. Here, we present the structure of the membrane-embedded LUJV spike complex determined by cryo-electron microscopy. Analysis of the structure suggested that a single NRP2 molecule is bound at the apex of the trimeric spike and that multiple subunits of the trimer contact the receptor. The binding of NRP2 involves an intriguing arginine-methionine interaction, which we analyzed using quantum mechanical modeling methods. We compare the LUJV spike structure with the only other available structure of a complete arenaviral spike, which is the Lassa virus. The similarities and differences between them shed light on Arenavirus evolution, inform vaccine design, and provide information that will be useful in combating future Arenavirus outbreaks. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17428.map.gz | 32.1 MB | EMDB map data format | |
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Header (meta data) | emd-17428-v30.xml emd-17428.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17428_fsc.xml | 9.6 KB | Display | FSC data file |
Images | emd_17428.png | 102.5 KB | ||
Masks | emd_17428_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-17428.cif.gz | 5.9 KB | ||
Others | emd_17428_additional_1.map.gz emd_17428_half_map_1.map.gz emd_17428_half_map_2.map.gz | 53.8 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17428 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17428 | HTTPS FTP |
-Validation report
Summary document | emd_17428_validation.pdf.gz | 877.3 KB | Display | EMDB validaton report |
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Full document | emd_17428_full_validation.pdf.gz | 876.9 KB | Display | |
Data in XML | emd_17428_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_17428_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17428 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17428 | HTTPS FTP |
-Related structure data
Related structure data | 8p4tMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17428.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Unfiltered map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17428_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered map
File | emd_17428_additional_1.map | ||||||||||||
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Annotation | Unfiltered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered map
File | emd_17428_half_map_1.map | ||||||||||||
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Annotation | Unfiltered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered map
File | emd_17428_half_map_2.map | ||||||||||||
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Annotation | Unfiltered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Spike complex from the Lujo virus
Entire | Name: Spike complex from the Lujo virus |
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Components |
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-Supramolecule #1: Spike complex from the Lujo virus
Supramolecule | Name: Spike complex from the Lujo virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Lujo mammarenavirus |
-Macromolecule #1: Glycoprotein
Macromolecule | Name: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mammarenavirus lujoense |
Molecular weight | Theoretical: 19.017572 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SSLLSGFNLE TVHFNMSLLS SIPMVSEQQH CIQHNHSSIT FSLLTNKSDL EKCNFTRLQA VDRVIFDLFR EFHHRVGDFP VTSDLKCSH NTSYRVIEYE VTKESLPRLQ EAVSTLFPDL HLSEDRFLQI QAHDDKNCTG LHPLNYLRLL KENSETHYKV R KLM UniProtKB: Glycoprotein |
-Macromolecule #2: Glycoprotein
Macromolecule | Name: Glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mammarenavirus lujoense |
Molecular weight | Theoretical: 28.267627 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KLFQWSLSDE TGSPLPGGHC LERWLIFASD IKCFDNAAIA KCNKEHDEEF CDMLRLFDYN KASIAKLRGE ASSSINLLSG RINAIISDT LLMRSSLKRL MGIPYCNYTK FWYLNHTKLG IHSLPRCWLV SNGSYLNETK FTHDMEDEAD KLLTEMLKKE Y VRRQEKTP ...String: KLFQWSLSDE TGSPLPGGHC LERWLIFASD IKCFDNAAIA KCNKEHDEEF CDMLRLFDYN KASIAKLRGE ASSSINLLSG RINAIISDT LLMRSSLKRL MGIPYCNYTK FWYLNHTKLG IHSLPRCWLV SNGSYLNETK FTHDMEDEAD KLLTEMLKKE Y VRRQEKTP ITLMDILMFS VSFYMFSVTL CICNIPTHRH ITGLPCPKPH RLRKNGTCAC GFFKSINRST GWAKHGGDYK DD DDKGSGT UniProtKB: Glycoprotein |
-Macromolecule #3: Glycoprotein
Macromolecule | Name: Glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mammarenavirus lujoense |
Molecular weight | Theoretical: 6.501998 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGQIVAVFQA IPEILNEAIN IVIIVIIMFT LIKGVFNLYK SGLFQLVIFL LLCGKRCD UniProtKB: Glycoprotein |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 21 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #8: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 8 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |