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- EMDB-9393: Electron Cryo-Microscopy Of Chikungunya VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-9393
TitleElectron Cryo-Microscopy Of Chikungunya VLP
Map dataChikungunya VLP
Sample
  • Virus: Chikungunya virus
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsChikungunya / virus-like particle / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / 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 E3 glycoprotein ...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 E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus (strain 37997) / Chikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsBasore K / Fremont DH
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 6, 2024-
Current statusNov 6, 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-6nk5
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6nk5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9393.png

Downloads & links

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Map

FileDownload / File: emd_9393.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya VLP
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-3.4880087 - 6.02024
Average (Standard dev.)0.0462273 (±0.5697404)
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-3.4886.0200.046

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Supplemental data

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Sample components

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Entire : Chikungunya virus

EntireName: Chikungunya virus
Components
  • Virus: Chikungunya virus
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Produced by PaxVax Corporation, Redwood CA, USA. / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: 37997 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus (strain 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 #2: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus (strain 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 #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus (strain 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 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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

Concentration0.33 mg/mL
BufferpH: 7.2
Component:
ConcentrationName
218.0 mMsucrose
10.0 mMpotassium phosphate
25.0 mMcitrate
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12 / 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

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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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8888
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0-beta) / Number images used: 8113
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
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6nk5:
Electron Cryo-Microscopy Of Chikungunya VLP

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