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- PDB-6jo8: The complex structure of CHIKV envelope glycoprotein bound to hum... -

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Basic information

Entry
Database: PDB / ID: 6jo8
TitleThe complex structure of CHIKV envelope glycoprotein bound to human MXRA8
Components
  • CHIKV E1
  • Matrix remodeling-associated protein 8
  • Togavirin
KeywordsVIRAL PROTEIN / Arthritogenic alphaviruses / receptor / MXRA8 / Chikungunya virus
Function / homology
Function and homology information


establishment of glial blood-brain barrier / protein metabolic process => GO:0019538 / togavirin / T=4 icosahedral viral capsid / ciliary membrane / host cell membrane / bicellular tight junction / viral process / post-translational protein modification / Post-translational protein phosphorylation ...establishment of glial blood-brain barrier / protein metabolic process => GO:0019538 / togavirin / T=4 icosahedral viral capsid / ciliary membrane / host cell membrane / bicellular tight junction / viral process / post-translational protein modification / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / viral capsid / host cell cytoplasm / membrane => GO:0016020 / cell adhesion / endoplasmic reticulum lumen / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / extracellular exosome / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Helix Hairpins - #2230 / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, A domain / 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 B / Helix Hairpins - #2230 / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, A domain / 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 / Helix Hairpins / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Polyprotein / Togavirin / Matrix remodeling-associated protein 8
Similarity search - Component
Biological speciesChikungunya virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.495 Å
AuthorsSong, H. / Zhao, Z. / Qi, J. / Gao, F. / Gao, F.G.
CitationJournal: Cell / Year: 2019
Title: Molecular Basis of Arthritogenic Alphavirus Receptor MXRA8 Binding to Chikungunya Virus Envelope Protein.
Authors: Hao Song / Zhennan Zhao / Yan Chai / Xiyue Jin / Changyao Li / Fei Yuan / Sheng Liu / Zhengrong Gao / Haiyuan Wang / Jian Song / Leonardo Vazquez / Yanfang Zhang / Shuguang Tan / Carlos M ...Authors: Hao Song / Zhennan Zhao / Yan Chai / Xiyue Jin / Changyao Li / Fei Yuan / Sheng Liu / Zhengrong Gao / Haiyuan Wang / Jian Song / Leonardo Vazquez / Yanfang Zhang / Shuguang Tan / Carlos M Morel / Jinghua Yan / Yi Shi / Jianxun Qi / Feng Gao / George F Gao /
Abstract: Arthritogenic alphaviruses, such as Chikungunya virus (CHIKV), cause severe and debilitating rheumatic diseases worldwide, resulting in severe morbidity and economic costs. Recently, MXRA8 was ...Arthritogenic alphaviruses, such as Chikungunya virus (CHIKV), cause severe and debilitating rheumatic diseases worldwide, resulting in severe morbidity and economic costs. Recently, MXRA8 was reported as an entry receptor. Here, we present the crystal structures of the mouse MXRA8, human MXRA8 in complex with the CHIKV E protein, and the cryo-electron microscopy structure of human MXRA8 and CHIKV virus-like particle. MXRA8 has two Ig-like domains with unique structural topologies. This receptor binds in the "canyon" between two protomers of the E spike on the surface of the virion. The atomic details at the interface between the two binding entities reveal that both the two domains and the hinge region of MXRA8 are involved in interaction with CHIKV E1-E2 residues from two protomers. Notably, the stalk region of MXRA8 is critical for CHIKV virus entry. This finding provides important information regarding the development of therapeutic countermeasures against those arthritogenic alphaviruses.
History
DepositionMar 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Togavirin
B: CHIKV E1
C: Togavirin
D: CHIKV E1
E: Togavirin
F: CHIKV E1
M: Matrix remodeling-associated protein 8
N: Matrix remodeling-associated protein 8
O: Matrix remodeling-associated protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,67913
Polymers366,1859
Non-polymers1,4944
Water0
1
A: Togavirin
B: CHIKV E1
O: Matrix remodeling-associated protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7075
Polymers122,0623
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Togavirin
D: CHIKV E1
N: Matrix remodeling-associated protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4864
Polymers122,0623
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Togavirin
F: CHIKV E1
M: Matrix remodeling-associated protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4864
Polymers122,0623
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.790, 208.790, 299.739
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Togavirin / / CHIKV p62


Mass: 45882.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high5 / References: UniProt: C8YZ73, togavirin
#2: Protein CHIKV E1


Mass: 46030.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high5 / References: UniProt: A4L787
#3: Protein Matrix remodeling-associated protein 8 / MXRA8 / Limitrin


Mass: 30148.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MXRA8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRK3
#4: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.15 Å3/Da / Density % sol: 76.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.8M Ammomium phophate dibasic, 0.1M sodium acetate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97893 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 3.49→50.15 Å / Num. obs: 95731 / % possible obs: 100 % / Redundancy: 130.4 % / CC1/2: 0.999 / Rpim(I) all: 0.042 / Rsym value: 0.047 / Net I/σ(I): 21
Reflection shellResolution: 3.49→3.61 Å / Redundancy: 127 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9457 / CC1/2: 0.642 / Rpim(I) all: 0.802 / Rsym value: 0.9022 / % possible all: 100

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Processing

Software
NameClassificationNB
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N40

3n40


Resolution: 3.495→50.15 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 4643 4.86 %
Rwork0.2484 90872 -
obs0.2495 95515 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 497.11 Å2 / Biso mean: 202.241 Å2 / Biso min: 74.9 Å2
Refinement stepCycle: LAST / Resolution: 3.495→50.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23406 0 98 0 23504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4954-3.53510.46771560.44642776293292
3.5351-3.57670.43451740.434929643138100
3.5767-3.62030.37261200.413730373157100
3.6203-3.66610.35981570.397330233180100
3.6661-3.71440.38361560.38929703126100
3.7144-3.76520.43651180.371230423160100
3.7652-3.8190.37211420.348129983140100
3.819-3.8760.36721750.334430013176100
3.876-3.93650.30771650.320930063171100
3.9365-4.0010.30741610.303629813142100
4.001-4.070.28651340.294330193153100
4.07-4.1440.28781400.285830353175100
4.144-4.22360.29611650.265930063171100
4.2236-4.30980.29231800.256129963176100
4.3098-4.40350.26391170.236730473164100
4.4035-4.50580.25551400.238930313171100
4.5058-4.61840.24921580.226330293187100
4.6184-4.74320.23891500.222230543204100
4.7432-4.88270.26591580.21429993157100
4.8827-5.04010.25061740.218730063180100
5.0401-5.22010.24681770.222630623239100
5.2201-5.42890.2641610.229729893150100
5.4289-5.67560.3031470.226830453192100
5.6756-5.97440.25951750.238730583233100
5.9744-6.3480.30361360.251230903226100
6.348-6.8370.27451530.237530483201100
6.837-7.5230.27821840.229930523236100
7.523-8.60690.22351510.216431203271100
8.6069-10.82580.20971430.207531393282100
10.8258-50.15490.24771760.237532493425100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0498-0.97560.26980.5-0.64211.35990.1785-0.15910.06030.0789-0.0041-0.1897-0.00680.34320.00060.7509-0.1582-0.12730.9450.02991.136727.338124.021339.2505
20.07190.0243-0.12380.73170.35631.1144-0.1536-0.41790.13560.51790.3749-0.13560.68740.13810.09391.6330.0168-0.24361.04470.12811.009937.1563-12.869848.9617
30.10560.09260.03670.247-0.32850.7735-0.08460.02580.3057-0.04290.25870.3499-0.01460.176-01.3795-0.4915-0.06951.5817-0.08571.301756.318246.995448.9666
40.38540.2294-0.00780.1511-0.09030.7077-0.1023-0.3448-0.15340.139-0.10150.0376-0.11050.5103-0.00171.5249-0.54380.03932.0837-0.23731.467937.84642.672382.5852
50.2636-0.2395-0.11290.4867-0.31580.702-0.0381-0.149-0.147-0.07280.06920.05720.12170.8186-00.9156-0.0139-0.03332.1306-0.05061.299563.425219.212930.7913
60.3303-0.29590.09320.082-0.22360.36870.0761-0.4921-0.3033-0.005-0.1831-0.1840.43640.6959-0.33020.79040.266-0.25942.84380.16361.259392.113519.471356.4594
70.32010.52060.31730.96540.55840.48420.125-0.0507-0.09920.0787-0.177-0.07340.24970.098401.40750.0459-0.12991.06840.0581.285632.66835.936911.3528
80.65570.1017-0.02150.1899-0.13540.21220.1165-0.47460.1551-0.54560.1445-0.1686-0.1240.9097-01.6666-0.4941-0.02622.62110.12321.724985.157345.24122.9967
90.37170.10040.26230.2685-0.02340.1636-0.4636-0.48780.1810.23210.20710.38140.20080.1787-02.7236-0.1685-0.091.77260.08791.960724.192362.220347.2326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA5 - 405
2X-RAY DIFFRACTION2chain BB-1 - 391
3X-RAY DIFFRACTION3chain CC68 - 405
4X-RAY DIFFRACTION4chain DD-1 - 391
5X-RAY DIFFRACTION5chain EE68 - 405
6X-RAY DIFFRACTION6chain FF-1 - 391
7X-RAY DIFFRACTION7chain MM33 - 292
8X-RAY DIFFRACTION8chain NN33 - 292
9X-RAY DIFFRACTION9chain OO33 - 292

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