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- EMDB-24116: CryoEM structure of Venezuelan equine encephalitis virus VLP in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-24116
TitleCryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor
Map dataSharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Sample
  • Complex: Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
    • Complex: Venezuelan equine encephalitis VLP
      • Protein or peptide: E1 envelope glycoprotein
      • Protein or peptide: E2 envelope glycoprotein
      • Protein or peptide: Capsid
    • Organelle or cellular component: LDLRAD3 receptor domain 1
      • Protein or peptide: Low-density lipoprotein receptor class A domain-containing protein 3
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


regulation of protein processing / T=4 icosahedral viral capsid / receptor-mediated endocytosis / amyloid-beta binding / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / 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 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / membrane / plasma membrane / cytoplasm
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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBasore K / Nelson CA / Fremont DH / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateNov 10, 2021-
Current statusNov 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n1h
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7n1h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24116.png

Downloads & links

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Map

FileDownload / File: emd_24116.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 700 pix.
= 770. Å		1.1 Å/pix.
x 700 pix.
= 770. Å		1.1 Å/pix.
x 700 pix.
= 770. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.01069855 - 2.1788745
Average (Standard dev.)0.011070774 (±0.07157769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-349-349-349
Dimensions700700700
Spacing700700700
CellA=B=C: 770.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z770.000770.000770.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-349-349-349
NC/NR/NS700700700
D min/max/mean-0.0112.1790.011

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Supplemental data

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Additional map: Unsharpened electron microscopy map of Venezuelan equine encephalitis...

Fileemd_24116_additional_1.map
AnnotationUnsharpened electron microscopy map of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map #1 of Venezuelan equine encephalitis...

Fileemd_24116_half_map_1.map
AnnotationUnsharpened half map #1 of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map #2 of Venezuelan equine encephalitis...

Fileemd_24116_half_map_2.map
AnnotationUnsharpened half map #2 of Venezuelan equine encephalitis VLP in complex with domain 1 of LDLRAD3 receptor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Venezuelan equine encephalitis VLP in complex with domain 1 of th...

EntireName: Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
Components
  • Complex: Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
    • Complex: Venezuelan equine encephalitis VLP
      • Protein or peptide: E1 envelope glycoprotein
      • Protein or peptide: E2 envelope glycoprotein
      • Protein or peptide: Capsid
    • Organelle or cellular component: LDLRAD3 receptor domain 1
      • Protein or peptide: Low-density lipoprotein receptor class A domain-containing protein 3
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Venezuelan equine encephalitis VLP in complex with domain 1 of th...

SupramoleculeName: Venezuelan equine encephalitis VLP in complex with domain 1 of the LDLRAD3 receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Venezuelan equine encephalitis virus / Strain: TC-83
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #3: Venezuelan equine encephalitis VLP

SupramoleculeName: Venezuelan equine encephalitis VLP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4
Details: Virus like particle produce in HEK293F cells by recombinant expression of structural proteins.
Source (natural)Organism: Venezuelan equine encephalitis virus / Strain: TC-83
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #2: LDLRAD3 receptor domain 1

SupramoleculeName: LDLRAD3 receptor domain 1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Receptor fragment produced asserted Fc fusion in Expi293F cells and released by HRV 3C Cleavage.
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F

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Macromolecule #1: 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: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 4.312861 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ECNIPGNFMC SNGRCIPGAW QCDGLPDCFD KSDEKECPK

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Macromolecule #2: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus
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

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Macromolecule #3: E2 envelope glycoprotein

MacromoleculeName: E2 envelope glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus
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

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Macromolecule #4: Capsid

MacromoleculeName: Capsid / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus
Molecular weightTheoretical: 18.19584 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KRQRMVMKLE SDKTFPIMLE GKINGYACVV GGKLFRPMHV EGKIDNDVLA ALKTKKASKY DLEYADVPQN MRADTFKYTH EKPQGYYSW HHGAVQYENG RFTVPKGVGA KGDSGRPILD NQGRVVAIVL GGVNEGSRTA LSVVMWNEKG VTVKYTPENC E QW

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j0c

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 12216
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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