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- EMDB-9394: Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse... -

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Basic information

Entry
Database: EMDB / ID: EMD-9394
TitleElectron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor
Map dataChikungunya VLP in complex with mouse Mxra8 receptor
Sample
  • Complex: Chikungunya virus like particle with Mxra8
    • Complex: Chikungunya virus like particle
      • Protein or peptide: E1 glycoprotein
      • Protein or peptide: E2 glycoprotein
      • Protein or peptide: Capsid protein
    • Complex: Mxra8 receptor
      • Protein or peptide: Matrix remodeling-associated protein 8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsChikungunya / virus-like particle / viral receptor / Mxra8 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


establishment of glial blood-brain barrier / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / togavirin / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / cell adhesion ...establishment of glial blood-brain barrier / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / togavirin / T=4 icosahedral viral capsid / ciliary membrane / bicellular tight junction / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / cell adhesion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / cell surface / proteolysis / RNA binding / nucleus / membrane / cytoplasm
Similarity search - Function
Matrix remodeling-associated protein 8 / 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 ...Matrix remodeling-associated protein 8 / 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. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin E-set / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Matrix remodeling-associated protein 8
Similarity search - Component
Biological speciesChikungunya virus (strain 37997) / Mus musculus (house mouse) / Chikungunya virus strain Senegal 37997
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsBasore K / Kim AS
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: Cell / Year: 2019
Title: Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor.
Authors: Katherine Basore / Arthur S Kim / Christopher A Nelson / Rong Zhang / Brittany K Smith / Carla Uranga / Lo Vang / Ming Cheng / Michael L Gross / Jonathan Smith / Michael S Diamond / Daved H Fremont /
Abstract: Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal ...Mxra8 is a receptor for multiple arthritogenic alphaviruses that cause debilitating acute and chronic musculoskeletal disease in humans. Herein, we present a 2.2 Å resolution X-ray crystal structure of Mxra8 and 4 to 5 Å resolution cryo-electron microscopy reconstructions of Mxra8 bound to chikungunya (CHIKV) virus-like particles and infectious virus. The Mxra8 ectodomain contains two strand-swapped Ig-like domains oriented in a unique disulfide-linked head-to-head arrangement. Mxra8 binds by wedging into a cleft created by two adjacent CHIKV E2-E1 heterodimers in one trimeric spike and engaging a neighboring spike. Two binding modes are observed with the fully mature VLP, with one Mxra8 binding with unique contacts. Only the high-affinity binding mode was observed in the complex with infectious CHIKV, as viral maturation and E3 occupancy appear to influence receptor binding-site usage. Our studies provide insight into how Mxra8 binds CHIKV and creates a path for developing alphavirus entry inhibitors.
History
DepositionJan 4, 2019-
Header (metadata) releaseFeb 27, 2019-
Map releaseMay 22, 2019-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nk6
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nk6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9394.png

Downloads & links

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Map

FileDownload / File: emd_9394.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya VLP in complex with mouse Mxra8 receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 600 pix.
= 841.8 Å		1.4 Å/pix.
x 600 pix.
= 841.8 Å		1.4 Å/pix.
x 600 pix.
= 841.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-3.9830904 - 6.3030233
Average (Standard dev.)0.05519889 (±0.63631827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 841.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z841.800841.800841.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-3.9836.3030.055

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Supplemental data

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Sample components

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Entire : Chikungunya virus like particle with Mxra8

EntireName: Chikungunya virus like particle with Mxra8
Components
  • Complex: Chikungunya virus like particle with Mxra8
    • Complex: Chikungunya virus like particle
      • Protein or peptide: E1 glycoprotein
      • Protein or peptide: E2 glycoprotein
      • Protein or peptide: Capsid protein
    • Complex: Mxra8 receptor
      • Protein or peptide: Matrix remodeling-associated protein 8
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Chikungunya virus like particle with Mxra8

SupramoleculeName: Chikungunya virus like particle with Mxra8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: VLP Produced by PaxVax Corporation, Redwood CA, USA. Mouse Mxra8 produced in HEK293 cells.

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Supramolecule #2: Chikungunya virus like particle

SupramoleculeName: Chikungunya virus like particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Chikungunya virus (strain 37997) / Strain: 37997

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Supramolecule #3: Mxra8 receptor

SupramoleculeName: Mxra8 receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Matrix remodeling-associated protein 8

MacromoleculeName: Matrix remodeling-associated protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 30.819457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLHDRQRV VHWDLSGGPG SQRRRLVDMY SAGEQRVYEP RDRDRLLLSP SAFHDGNFS LLIRAVDRGD EGVYTCNLHH HYCHLDESLA VRLEVTEDPL LSRAYWDGEK EVLVVAHGAP ALMTCINRAH V WTDRHLEE ...String:
SSSLVSESVV SLAAGTQAVL RCQSPRMVWT QDRLHDRQRV VHWDLSGGPG SQRRRLVDMY SAGEQRVYEP RDRDRLLLSP SAFHDGNFS LLIRAVDRGD EGVYTCNLHH HYCHLDESLA VRLEVTEDPL LSRAYWDGEK EVLVVAHGAP ALMTCINRAH V WTDRHLEE AQQVVHWDRQ LPGVSHDRAD RLLDLYASGE RRAYGPPFLR DRVSVNTNAF ARGDFSLRID ELERADEGIY SC HLHHHYC GLHERRVFHL QVTEPAFEPP SA

UniProtKB: Matrix remodeling-associated protein 8

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Macromolecule #2: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 47.346715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELQSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVAAYAN GDHAVTVKDA K FVVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNIP ISIDIPDAAF TRVVDAPSVT DMSCEVPACT HSSDFGGVAI IKY TASKKG KCAVHSMTNA VTIREADVEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAACHPPKDH IVNYPASHTT LGVQ DISTT AMSWVQKITG GVGLIVAVAA LILIVVLCVS FSRH

UniProtKB: Structural polyprotein

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Macromolecule #3: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 46.858312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP ...String:
NFNVYKATRP YLAHCPDCGE GHSCHSPIAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDSHT PADAERAGLL VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDSRKISH TCTHPFHHEP PVIGRERFHS RPQHGKELPC STYVQSTAAT A EEIEVHMP PDTPDRTLMT QQSGNVKITV NGQTVRYKCN CGGSNEGLTT TDKVINNCKI DQCHAAVTNH KNWQYNSPLV PR NAELGDR KGKIHIPFPL ANVTCRVPKA RNPTVTYGKN QVTMLLYPDH PTLLSYRNMG QEPNYHEEWV THKKEVTLTV PTE GLEVTW GNNEPYKYWP QMSTNGTAHG HPHEIILYYY ELYPTMTVVI VSVASFVLLS MVGTAVGMCV CARRRCITPY ELTP GATVP FLLSLLCCVR TTKA

UniProtKB: Structural polyprotein

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Macromolecule #4: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 16.458701 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NDCIFEVKHE GKVMGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW

UniProtKB: Structural polyprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 12 / 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

Concentration0.33 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
218.0 mMsucrose
10.0 mMpotassium phosphate
25.0 mMcitrate
150.0 mMsodium chlorideNaCl
25.0 mMHEPESC8H18N2O4S
1.0 mMsodium azideNaN3
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 120 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: 0.458 mbar.l/s O2 and 0.11 mbar.l/s H2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details0.33 mg/mL VLP + 15 mg/mL Mxra8

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.3 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0-beta) / Number images used: 22486
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN (ver. 10)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3n42

chain_id: B, residue_range: 5-342, source_name: PDB, initial_model_type: experimental model

3n42

chain_id: F, residue_range: 1-393, source_name: PDB, initial_model_type: experimental model

3j0c

chain_id: A, residue_range: 394-442, source_name: PDB, initial_model_type: experimental model

3j0c

chain_id: B, residue_range: 394-423, source_name: PDB, initial_model_type: experimental model

5h23

chain_id: A, residue_range: 111-261, source_name: PDB, initial_model_type: experimental model

6nk3

chain_id: A, residue_range: 39-291, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6nk6:
Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor

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