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

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Basic information

Entry
Database: PDB / ID: 7pvd
TitleStructure of the membrane soluble spike complex from the Lassa virus in a C1-symmetric map focused on the ectodomain
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 / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 2, 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 1.3Nov 20, 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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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)179,91728
Polymers171,4436
Non-polymers8,47422
Water00
1


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

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_1THRTHRLEULEUAD59 - 24459 - 244
d_12ens_1NAGNAGNAGNAGDG1
d_13ens_1NAGNAGNAGNAGDG1
d_14ens_1NAGNAGNAGNAGEH1
d_15ens_1NAGNAGNAGNAGEH1
d_16ens_1NAGNAGNAGNAGFI1
d_17ens_1NAGNAGNAGNAGFI1
d_18ens_1NAGNAGNAGNAGAW301
d_19ens_1NAGNAGNAGNAGAX302
d_21ens_1THRTHRLEULEUBE59 - 24459 - 244
d_22ens_1NAGNAGNAGNAGGJ1
d_23ens_1NAGNAGNAGNAGGJ1
d_24ens_1NAGNAGNAGNAGHK1
d_25ens_1NAGNAGNAGNAGHK1
d_26ens_1NAGNAGNAGNAGIL1
d_27ens_1NAGNAGNAGNAGIL1
d_28ens_1NAGNAGNAGNAGBY301
d_29ens_1NAGNAGNAGNAGBZ302
d_31ens_1THRTHRLEULEUCF59 - 24459 - 244
d_32ens_1NAGNAGNAGNAGJM1
d_33ens_1NAGNAGNAGNAGJM1
d_34ens_1NAGNAGNAGNAGKN1
d_35ens_1NAGNAGNAGNAGKN1
d_36ens_1NAGNAGNAGNAGLO1
d_37ens_1NAGNAGNAGNAGLO1
d_38ens_1NAGNAGNAGNAGCAA301
d_39ens_1NAGNAGNAGNAGCBA302
d_11ens_2GLYGLYTYRTYRaA260 - 4191 - 160
d_12ens_2NAGNAGNAGNAGaQ601
d_13ens_2NAGNAGNAGNAGaR602
d_21ens_2GLYGLYTYRTYRbB260 - 4191 - 160
d_22ens_2NAGNAGNAGNAGbS601
d_23ens_2NAGNAGNAGNAGbT602
d_31ens_2GLYGLYTYRTYRcC260 - 4191 - 160
d_32ens_2NAGNAGNAGNAGcU601
d_33ens_2NAGNAGNAGNAGcV602

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.495446867326, 0.868636980216, 0.00148265232979), (-0.868636994892, -0.495442535801, -0.00254260157837), (-0.00147402872695, -0.00254761065108, 0.99999566845)83.0496514528, 314.424637768, 0.496092833596
2given(-0.497374695822, -0.867516252177, -0.00582787825399), (0.867535827227, -0.497363311461, -0.00336524739661), (2.08339819564E-5, -0.00672968208231, 0.999977355216)315.071404858, 84.094801472, 1.55428020834
3given(-0.505248675756, -0.862948967834, -0.00654633948515), (0.862956741057, -0.50527184638, 0.00245444884917), (-0.00542574513968, -0.0044091007572, 0.999975560261)315.620131177, 84.9378266278, 1.35925994585
4given(-0.493913639219, 0.869503572311, -0.0035853496076), (-0.869484954089, -0.493926559232, -0.00569813106555), (-0.00672544471233, 0.000303022887628, 0.999977338028)83.3732809408, 314.871770447, 1.19884504407

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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-(1-3)-beta-D- ...alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 1999.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-3DGlcpAb1-3DXylpa1-3DGlcpAb1-3DXylpa1-3DGlcpAb1-3DXylpa1-3DGlcpAb1-3DXylpa1-3DGlcpAb1-3DXylpa1-3DGlcpAb1-3DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,13,12/[a212h-1a_1-5][a2122A-1b_1-5]/1-2-1-2-1-2-1-2-1-2-1-2-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1_f3-g1_g3-h1_h3-i1_i3-j1_j3-k1_k3-l1_l3-m1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][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.: 12 / 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
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: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: OTHER / Num. of particles: 103416 / Details: Low-pass filtering according to map-model FSC / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00379079
ELECTRON MICROSCOPYf_angle_d0.66912275
ELECTRON MICROSCOPYf_chiral_restr0.04811471
ELECTRON MICROSCOPYf_plane_restr0.00441497
ELECTRON MICROSCOPYf_dihedral_angle_d14.21143292
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints0.121005440482
ens_1d_3BELECTRON MICROSCOPYNCS constraints0.121005579153
ens_2d_2cELECTRON MICROSCOPYNCS constraints0.000692388245149
ens_2d_3cELECTRON MICROSCOPYNCS constraints0.100208413449

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