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- PDB-7n1h: CryoEM structure of Venezuelan equine encephalitis virus VLP in c... -

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Basic information

Entry
Database: PDB / ID: 7n1h
TitleCryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor
Components
  • Capsid
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
  • Low-density lipoprotein receptor class A domain-containing protein 3
KeywordsVIRUS LIKE PARTICLE / VEEV / viral envelope / host receptor / low-density lipoprotein receptor type-A module / LDLRAD3 / encephalitic alphavirus / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane ...regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / membrane / plasma membrane
Similarity search - Function
: / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein ...: / Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Low-density lipoprotein receptor class A domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Venezuelan equine encephalitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBasore, K. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nature / Year: 2021
Title: Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor.
Authors: Katherine Basore / Hongming Ma / Natasha M Kafai / Samantha Mackin / Arthur S Kim / Christopher A Nelson / Michael S Diamond / Daved H Fremont /
Abstract: LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present ...LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV), a New World alphavirus that causes severe neurological disease in humans. Here we present near-atomic-resolution cryo-electron microscopy reconstructions of VEEV virus-like particles alone and in a complex with the ectodomains of LDLRAD3. Domain 1 of LDLRAD3 is a low-density lipoprotein receptor type-A module that binds to VEEV by wedging into a cleft created by two adjacent E2-E1 heterodimers in one trimeric spike, and engages domains A and B of E2 and the fusion loop in E1. Atomic modelling of this interface is supported by mutagenesis and anti-VEEV antibody binding competition assays. Notably, VEEV engages LDLRAD3 in a manner that is similar to the way that arthritogenic alphaviruses bind to the structurally unrelated MXRA8 receptor, but with a much smaller interface. These studies further elucidate the structural basis of alphavirus-receptor interactions, which could inform the development of therapies to mitigate infection and disease against multiple members of this family.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification ..._em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-24116
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
O: Low-density lipoprotein receptor class A domain-containing protein 3
M: Low-density lipoprotein receptor class A domain-containing protein 3
N: Low-density lipoprotein receptor class A domain-containing protein 3
P: Low-density lipoprotein receptor class A domain-containing protein 3
D: E1 envelope glycoprotein
H: E2 envelope glycoprotein
L: Capsid
C: E1 envelope glycoprotein
G: E2 envelope glycoprotein
K: Capsid
B: E1 envelope glycoprotein
F: E2 envelope glycoprotein
J: Capsid
A: E1 envelope glycoprotein
E: E2 envelope glycoprotein
I: Capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,22828
Polymers470,29816
Non-polymers1,93012
Water00
1
O: Low-density lipoprotein receptor class A domain-containing protein 3
M: Low-density lipoprotein receptor class A domain-containing protein 3
N: Low-density lipoprotein receptor class A domain-containing protein 3
P: Low-density lipoprotein receptor class A domain-containing protein 3
D: E1 envelope glycoprotein
H: E2 envelope glycoprotein
L: Capsid
C: E1 envelope glycoprotein
G: E2 envelope glycoprotein
K: Capsid
B: E1 envelope glycoprotein
F: E2 envelope glycoprotein
J: Capsid
A: E1 envelope glycoprotein
E: E2 envelope glycoprotein
I: Capsid
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)28,333,6821680
Polymers28,217,883960
Non-polymers115,799720
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: Low-density lipoprotein receptor class A domain-containing protein 3
M: Low-density lipoprotein receptor class A domain-containing protein 3
N: Low-density lipoprotein receptor class A domain-containing protein 3
P: Low-density lipoprotein receptor class A domain-containing protein 3
D: E1 envelope glycoprotein
H: E2 envelope glycoprotein
L: Capsid
C: E1 envelope glycoprotein
G: E2 envelope glycoprotein
K: Capsid
B: E1 envelope glycoprotein
F: E2 envelope glycoprotein
J: Capsid
A: E1 envelope glycoprotein
E: E2 envelope glycoprotein
I: Capsid
hetero molecules
x 5


  • icosahedral pentamer
  • 2.36 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,361,140140
Polymers2,351,49080
Non-polymers9,65060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
O: Low-density lipoprotein receptor class A domain-containing protein 3
M: Low-density lipoprotein receptor class A domain-containing protein 3
N: Low-density lipoprotein receptor class A domain-containing protein 3
P: Low-density lipoprotein receptor class A domain-containing protein 3
D: E1 envelope glycoprotein
H: E2 envelope glycoprotein
L: Capsid
C: E1 envelope glycoprotein
G: E2 envelope glycoprotein
K: Capsid
B: E1 envelope glycoprotein
F: E2 envelope glycoprotein
J: Capsid
A: E1 envelope glycoprotein
E: E2 envelope glycoprotein
I: Capsid
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 2.83 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)2,833,368168
Polymers2,821,78896
Non-polymers11,58072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 3 types, 12 molecules DCBAHGFELKJI

#2: Protein
E1 envelope glycoprotein / Togavirin


Mass: 47952.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98
#3: Protein
E2 envelope glycoprotein / Togavirin


Mass: 47113.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98
#4: Protein
Capsid / Togavirin


Mass: 18195.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98

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Protein/peptide / Non-polymers / Sugars , 3 types, 16 molecules OMNP

#1: Protein/peptide
Low-density lipoprotein receptor class A domain-containing protein 3


Mass: 4312.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldlrad3 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A2AR95
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: 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.: 8 / 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

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Details

Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptorCOMPLEX#1-#40RECOMBINANT
2LDLRAD3 receptor domain 1ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANTReceptor fragment produced asserted Fc fusion in Expi293F cells and released by HRV 3C Cleavage.
3Venezuelan equine encephalitis VLPCOMPLEX#2-#41RECOMBINANTVirus like particle produce in HEK293F cells by recombinant expression of structural proteins.
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Venezuelan equine encephalitis virus11036TC-83
31Mus musculus (house mouse)10090
43Venezuelan equine encephalitis virus11036TC-83
52Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293F
32Homo sapiens (human)9606Expi293F
43Homo sapiens (human)9606HEK293F
Details of virusEmpty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Mosquito
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12216 / Symmetry type: POINT

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