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- PDB-7puy: Structure of the membrane soluble spike complex from the Lassa vi... -

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Basic information

Entry
Database: PDB / ID: 7puy
TitleStructure of the membrane soluble spike complex from the Lassa virus in a C3-symmetric map
Components
  • Glycoprotein G2
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Spike complex / glycoprotein
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 / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDiskin, R. / Katz, M.
Funding support1items
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 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification ..._em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
a: Glycoprotein G2
b: Glycoprotein G2
c: Glycoprotein G2
A: Pre-glycoprotein polyprotein GP complex
B: Pre-glycoprotein polyprotein GP complex
C: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,95633
Polymers171,4436
Non-polymers8,51327
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_1ens_2chain "a"
d_2ens_2chain "b"
d_3ens_2chain "c"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYLEULEUAD2 - 2202 - 220
d_12ens_1NAGNAGNAGNAGDG1
d_13ens_1NAGNAGNAGNAGDG1
d_14ens_1NAGNAGNAGNAGEH1
d_15ens_1NAGNAGNAGNAGEH1
d_16ens_1NAGNAGNAGNAGFI1
d_17ens_1NAGNAGNAGNAGFI1
d_18ens_1NAGNAGNAGNAGABA301
d_19ens_1NAGNAGNAGNAGACA302
d_110ens_1XYSXYSXYSXYSGJ1
d_111ens_1BDPBDPBDPBDPGJ2
d_112ens_1XYSXYSXYSXYSGJ1
d_21ens_1GLYGLYLEULEUBE2 - 2202 - 220
d_22ens_1NAGNAGNAGNAGHK1
d_23ens_1NAGNAGNAGNAGHK1
d_24ens_1NAGNAGNAGNAGIL1
d_25ens_1NAGNAGNAGNAGIL1
d_26ens_1NAGNAGNAGNAGJM1
d_27ens_1NAGNAGNAGNAGJM1
d_28ens_1NAGNAGNAGNAGBDA301
d_29ens_1NAGNAGNAGNAGBEA302
d_210ens_1XYSXYSXYSXYSKN1
d_211ens_1BDPBDPBDPBDPKN2
d_212ens_1XYSXYSXYSXYSKN1
d_31ens_1GLYGLYLEULEUCF2 - 2202 - 220
d_32ens_1NAGNAGNAGNAGLO1
d_33ens_1NAGNAGNAGNAGLO1
d_34ens_1NAGNAGNAGNAGMP1
d_35ens_1NAGNAGNAGNAGMP1
d_36ens_1NAGNAGNAGNAGNQ1
d_37ens_1NAGNAGNAGNAGNQ1
d_38ens_1NAGNAGNAGNAGCFA301
d_39ens_1NAGNAGNAGNAGCGA302
d_310ens_1XYSXYSXYSXYSOR1
d_311ens_1BDPBDPBDPBDPOR2
d_312ens_1XYSXYSXYSXYSOR1
d_11ens_2GLYGLYHISHISaA260 - 4481 - 189
d_12ens_2NAGNAGNAGNAGaS601
d_13ens_2NAGNAGNAGNAGaT602
d_14ens_2NAGNAGNAGNAGaU603
d_21ens_2GLYGLYHISHISbB260 - 4481 - 189
d_22ens_2NAGNAGNAGNAGbV601
d_23ens_2NAGNAGNAGNAGbW602
d_24ens_2NAGNAGNAGNAGbX603
d_31ens_2GLYGLYHISHIScC260 - 4481 - 189
d_32ens_2NAGNAGNAGNAGcY601
d_33ens_2NAGNAGNAGNAGcZ602
d_34ens_2NAGNAGNAGNAGcAA603

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.495544829548, -0.868581132734, -0.00146211033129), (0.868581072868, -0.495540489513, -0.00255795010878), (0.00149725233367, -0.00253754031085, 0.999995659553)314.275168962, 83.6637855222, -0.0082609186683
2given(-0.503502855697, 0.863993283607, 0.000692955181274), (-0.863988796194, -0.503502580501, 0.00291744404495), (0.00286955678208, 0.00087023589508, 0.999995504157)84.8554454089, 314.002903713, -0.474677131687
3given(-0.500899312566, -0.86550528539, -0.000692554798109), (0.865505125676, -0.500899703322, 0.000603854589148), (-0.000869539831422, -0.00029693937898, 0.999999577864)314.544725202, 84.261238855, -0.0441263650771
4given(-0.498614581233, 0.866819530106, -0.00272058995926), (-0.86682085374, -0.498618613329, -0.00104209617105), (-0.00225984610623, 0.00183865976523, 0.999995756204)84.3659901234, 314.409956277, 0.111118962655

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Components

#1: Protein Glycoprotein G2 / GP2


Mass: 28083.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: GPC, GP-C / Production host: Homo sapiens (human) / References: UniProt: P08669
#2: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 29064.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: GPC, GP-C / Production host: Homo sapiens (human) / References: UniProt: P08669
#3: 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.: 9
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
#4: Polysaccharide alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 458.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-3DGlcpAb1-3DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1a_1-5][a2122A-1b_1-5]/1-2-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15 / Source method: obtained synthetically / 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
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complete spike complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Lassa virus Josiah
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GRAPHENE OXIDE / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 73 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: OTHER / Num. of particles: 91903 / Details: Global low-pass filtering based on map-model FSC / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002410602
ELECTRON MICROSCOPYf_angle_d0.614814340
ELECTRON MICROSCOPYf_chiral_restr0.04341728
ELECTRON MICROSCOPYf_plane_restr0.00461746
ELECTRON MICROSCOPYf_dihedral_angle_d14.50873846
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EELECTRON MICROSCOPYNCS constraints0.000699837947628
ens_1d_3FELECTRON MICROSCOPYNCS constraints0.000698744983358
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.000701619202457
ens_2d_3CELECTRON MICROSCOPYNCS constraints0.000707785851087

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