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- PDB-5ft2: Sub-tomogram averaging of Lassa virus glycoprotein spike from vir... -

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Entry
Database: PDB / ID: 5ft2
TitleSub-tomogram averaging of Lassa virus glycoprotein spike from virus- like particles at pH 5
ComponentsPRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX
KeywordsCELL ADHESION / MEMBRANE PROTEIN / GLYCOPROTEIN / RECEPTOR BINDING / MEMBRANE FUSION
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
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLASSA VIRUS
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 16.4 Å
AuthorsLi, S. / Zhaoyang, S. / Pryce, R. / Parsy, M.L. / Fehling, S.K. / Schlie, K. / Siebert, C.A. / Garten, W. / Bowden, T.A. / Strecker, T. / Huiskonen, J.T.
Citation
Journal: PLoS Pathog / Year: 2016
Title: Acidic pH-Induced Conformations and LAMP1 Binding of the Lassa Virus Glycoprotein Spike.
Authors: Sai Li / Zhaoyang Sun / Rhys Pryce / Marie-Laure Parsy / Sarah K Fehling / Katrin Schlie / C Alistair Siebert / Wolfgang Garten / Thomas A Bowden / Thomas Strecker / Juha T Huiskonen /
Abstract: Lassa virus is an enveloped, bi-segmented RNA virus and the most prevalent and fatal of all Old World arenaviruses. Virus entry into the host cell is mediated by a tripartite surface spike complex, ...Lassa virus is an enveloped, bi-segmented RNA virus and the most prevalent and fatal of all Old World arenaviruses. Virus entry into the host cell is mediated by a tripartite surface spike complex, which is composed of two viral glycoprotein subunits, GP1 and GP2, and the stable signal peptide. Of these, GP1 binds to cellular receptors and GP2 catalyzes fusion between the viral envelope and the host cell membrane during endocytosis. The molecular structure of the spike and conformational rearrangements induced by low pH, prior to fusion, remain poorly understood. Here, we analyzed the three-dimensional ultrastructure of Lassa virus using electron cryotomography. Sub-tomogram averaging yielded a structure of the glycoprotein spike at 14-Å resolution. The spikes are trimeric, cover the virion envelope, and connect to the underlying matrix. Structural changes to the spike, following acidification, support a viral entry mechanism dependent on binding to the lysosome-resident receptor LAMP1 and further dissociation of the membrane-distal GP1 subunits.
#1: Journal: J Virol / Year: 2015
Title: Molecular Mechanism for LAMP1 Recognition by Lassa Virus.
Authors: Hadas Cohen-Dvashi / Nadav Cohen / Hadar Israeli / Ron Diskin /
Abstract: Lassa virus is a notorious human pathogen that infects many thousands of people each year in West Africa, causing severe viral hemorrhagic fevers and significant mortality. The surface glycoprotein ...Lassa virus is a notorious human pathogen that infects many thousands of people each year in West Africa, causing severe viral hemorrhagic fevers and significant mortality. The surface glycoprotein of Lassa virus mediates receptor recognition through its GP1 subunit. Here we report the crystal structure of GP1 from Lassa virus, which is the first representative GP1 structure for Old World arenaviruses. We identify a unique triad of histidines that forms a binding site for LAMP1, a known lysosomal protein recently discovered to be a critical receptor for internalized Lassa virus at acidic pH. We demonstrate that mutation of this histidine triad, which is highly conserved among Old World arenaviruses, impairs LAMP1 recognition. Our biochemical and structural data further suggest that GP1 from Lassa virus may undergo irreversible conformational changes that could serve as an immunological decoy mechanism. Together with a variable region that we identify on the surface of GP1, those could be two distinct mechanisms that Lassa virus utilizes to avoid antibody-based immune response.
IMPORTANCE: Structural data at atomic resolution for viral proteins is key for understanding their function at the molecular level and can facilitate novel avenues for combating viral infections. ...IMPORTANCE: Structural data at atomic resolution for viral proteins is key for understanding their function at the molecular level and can facilitate novel avenues for combating viral infections. Here we used X-ray protein crystallography to decipher the crystal structure of the receptor-binding domain (GP1) from Lassa virus. This is a pathogenic virus that causes significant illness and mortality in West Africa. This structure reveals the overall architecture of GP1 domains from the group of viruses known as the Old World arenaviruses. Using this structural information, we elucidated the mechanisms for pH switch and binding of Lassa virus to LAMP1, a recently identified host receptor that is critical for successful infection. Lastly, our structural analysis suggests two novel immune evasion mechanisms that Lassa virus may utilize to escape antibody-based immune response.
History
DepositionJan 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.details / _em_software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

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  • EMDB-3292
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Assembly

Deposited unit
B: PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6715
Polymers19,3801
Non-polymers1,2914
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX / GP1


Mass: 19379.693 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, UNP RESIDUES 75-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LASSA VIRUS / Strain: JOSIAH / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P08669
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: PURIFIED LASSA VIRUS VLPS AT PH 5 / Type: VIRUS
Buffer solutionName: 50 MM BUFFER OF SUCCINIC ACID, DIHYDROGEN PHOSPHATE AND GLYCINE (SPG)
pH: 5.2
Details: 50 MM BUFFER OF SUCCINIC ACID, DIHYDROGEN PHOSPHATE AND GLYCINE (SPG)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE-PROPANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 80, TEMPERATURE- 120, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING.,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Sep 25, 2014 / Details: SUPER-RESOLUTION COUNTING MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 6700 nm / Nominal defocus min: 2800 nm / Cs: 2 mm
Specimen holderTilt angle max: 45 ° / Tilt angle min: -45 °
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 16

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Processing

EM software
IDNameCategoryDetails
1UCSF Chimeramodel fitting
2Dynamo3D reconstruction
3IMOD3D reconstruction
4UCSF Chimeramodel fittingSegger
CTF correctionDetails: EACH TILTED IMAGE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionMethod: TEMPLATE BASED / Resolution: 16.4 Å / Num. of particles: 2578 / Nominal pixel size: 2.7 Å / Actual pixel size: 2.7 Å
Details: SUB-TOMOGRAM AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3292. (DEPOSITION ID: 14158).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 4ZJF
RefinementHighest resolution: 16.4 Å
Refinement stepCycle: LAST / Highest resolution: 16.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 84 23 1340

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