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- EMDB-31567: Structure of Venezuelan equine encephalitis virus with the recept... -

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Entry
Database: EMDB / ID: EMD-31567
TitleStructure of Venezuelan equine encephalitis virus with the receptor LDLRAD3
Map dataStructure of Venezuelan equine encephalitis virus with the receptor LDLRAD3
Sample
  • Complex: Venezuelan equine encephalitis virus (strain TC-83)
    • Complex: Venezuelan equine encephalitis virus (strain TC-83)
      • Protein or peptide: Capsid protein
      • Protein or peptide: Spike glycoprotein E1
      • Protein or peptide: assembly protein E3
      • Protein or peptide: Spike glycoprotein E2
    • Complex: LDLRAD3
      • Protein or peptide: Low-density lipoprotein receptor class A domain-containing protein 3
  • Ligand: CALCIUM ION
KeywordsVirus / Receptor / Complex / VIRUS LIKE PARTICLE / VIRUS LIKE PARTICLE-PROTEIN BINDING complex
Function / homology
Function and homology information


togavirin / regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity ...togavirin / regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / 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 speciesVenezuelan equine encephalitis virus (strain TC-83) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang X / Xiang Y
CitationJournal: Nature / Year: 2021
Title: Structure of Venezuelan equine encephalitis virus with its receptor LDLRAD3.
Authors: Bingting Ma / Cuiqing Huang / Jun Ma / Ye Xiang / Xinzheng Zhang /
Abstract: Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available ...Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines. At present, no vaccines or drugs are available that prevent or cure diseases caused by VEEV. Low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3) was recently identified as a receptor for the entry of VEEV into host cells. Here we present the cryo-electron microscopy structure of the LDLRAD3 extracellular domain 1 (LDLRAD3-D1) in complex with VEEV virus-like particles at a resolution of 3.0 Å. LDLRAD3-D1 has a cork-like structure and is inserted into clefts formed between adjacent VEEV E2-E1 heterodimers in the viral-surface trimer spikes through hydrophobic and polar contacts. Mutagenesis studies of LDLRAD3-D1 identified residues that are involved in the key interactions with VEEV. Of note, some of the LDLRAD3-D1 mutants showed a significantly increased binding affinity for VEEV, suggesting that LDLRAD3-D1 may serve as a potential scaffold for the development of inhibitors of VEEV entry. Our structures provide insights into alphavirus assembly and the binding of receptors to alphaviruses, which may guide the development of therapeutic countermeasures against alphaviruses.
History
DepositionJul 23, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by height
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7fff
  • Surface level: 0.02
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7fff
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31567.png

Downloads & links

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Map

FileDownload / File: emd_31567.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Venezuelan equine encephalitis virus with the receptor LDLRAD3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 Å		1.32 Å/pix.
x 360 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.15445258 - 0.22548763
Average (Standard dev.)0.0002711249 (±0.0060496232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.1540.2250.000

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Supplemental data

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Sample components

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Entire : Venezuelan equine encephalitis virus (strain TC-83)

EntireName: Venezuelan equine encephalitis virus (strain TC-83)
Components
  • Complex: Venezuelan equine encephalitis virus (strain TC-83)
    • Complex: Venezuelan equine encephalitis virus (strain TC-83)
      • Protein or peptide: Capsid protein
      • Protein or peptide: Spike glycoprotein E1
      • Protein or peptide: assembly protein E3
      • Protein or peptide: Spike glycoprotein E2
    • Complex: LDLRAD3
      • Protein or peptide: Low-density lipoprotein receptor class A domain-containing protein 3
  • Ligand: CALCIUM ION

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Supramolecule #1: Venezuelan equine encephalitis virus (strain TC-83)

SupramoleculeName: Venezuelan equine encephalitis virus (strain TC-83) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)

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Supramolecule #2: Venezuelan equine encephalitis virus (strain TC-83)

SupramoleculeName: Venezuelan equine encephalitis virus (strain TC-83) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: LDLRAD3

SupramoleculeName: LDLRAD3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 30.980801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSANKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK ...String:
MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSANKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK KASKYDLEYA DVPQNMRADT FKYTHEKPQG YYSWHHGAVQ YENGRFTVPK GVGAKGDSGR PILDNQGRVV AI VLGGVNE GSRTALSVVM WNEKGVTVKY TPENCEQW

UniProtKB: Structural polyprotein

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Macromolecule #2: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 47.952066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST ...String:
YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST AWTPFDRKIV QYAGEIYNYD FPEYGAGQPG AFGDIQSRTV SSSDLYANTN LVLQRPKAGA IHVPYTQAPS GF EQWKKDK APSLKFTAPF GCEIYTNPIR AENCAVGSIP LAFDIPDALF TRVSETPTLS AAECTLNECV YSSDFGGIAT VKY SASKSG KCAVHVPSGT ATLKEAAVEL TEQGSATIHF STANIHPEFR LQICTSYVTC KGDCHPPKDH IVTHPQYHAQ TFTA AVSKT AWTWLTSLLG GSAVIIIIGL VLATIVAMYV LTNQKHN

UniProtKB: Structural polyprotein

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Macromolecule #3: Low-density lipoprotein receptor class A domain-containing protein 3

MacromoleculeName: Low-density lipoprotein receptor class A domain-containing protein 3
type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.614737 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MWLLGPLCLL LSSAAESQLL PGNNFTNECN IPGNFMCSNG RCIPGAWQCD GLPDCFDKSD EKECPKAKSK

UniProtKB: Low-density lipoprotein receptor class A domain-containing protein 3

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Macromolecule #4: assembly protein E3

MacromoleculeName: assembly protein E3 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 6.488601 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SLVTTMCLLA NVTFPCAQPP ICYDRKPAET LAMLSVNVDN PGYDELLEAA VKCPGRKRR

UniProtKB: Structural polyprotein

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Macromolecule #5: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 47.113746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH ...String:
STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH LPGSEVDSSL VSLSGSSVTV TPPDGTSALV ECECGGTKIS ETINKTKQFS QCTKKEQCRA YRLQNDKWVY NS DKLPKAA GATLKGKLHV PFLLADGKCT VPLAPEPMIT FGFRSVSLKL HPKNPTYLIT RQLADEPHYT HELISEPAVR NFT VTEKGW EFVWGNHPPK RFWAQETAPG NPHGLPHEVI THYYHRYPMS TILGLSICAA IATVSVAAST WLFCRSRVAC LTPY RLTPN ARIPFCLAVL CCARTARA

UniProtKB: Structural polyprotein

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 726076
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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