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- PDB-6jo7: Crystal structure of mouse MXRA8 -

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Basic information

Entry
Database: PDB / ID: 6jo7
TitleCrystal structure of mouse MXRA8
ComponentsMatrix remodeling-associated protein 8
KeywordsPROTEIN BINDING / Arthritogenic alphaviruses / receptor / virus entry / Chikungunya virus
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 / ciliary membrane / bicellular tight junction / cell differentiation / cell adhesion / cell surface / nucleus / cytoplasm
Similarity search - Function
Matrix remodeling-associated protein 8 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Matrix remodeling-associated protein 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSong, H. / Zhao, Z. / Qi, J. / Gao, F. / Gao, G.F.
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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix remodeling-associated protein 8
B: Matrix remodeling-associated protein 8


Theoretical massNumber of molelcules
Total (without water)61,4492
Polymers61,4492
Non-polymers00
Water82946
1
A: Matrix remodeling-associated protein 8


Theoretical massNumber of molelcules
Total (without water)30,7241
Polymers30,7241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix remodeling-associated protein 8


Theoretical massNumber of molelcules
Total (without water)30,7241
Polymers30,7241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.446, 143.486, 196.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Matrix remodeling-associated protein 8 / Adipocyte-specific protein 3 / Dual Ig domain-containing cell adhesion molecule / DICAM / Limitrin


Mass: 30724.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mxra8, Asp3, Dicam / Plasmid: pet21a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9DBV4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.15 Å3/Da / Density % sol: 70.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M BICINE pH 8.5, 15% w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97894 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40460 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rsym value: 0.13 / Net I/σ(I): 22.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3978 / CC1/2: 0.691 / Rsym value: 1.919 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TT3

3tt3


Resolution: 2.4→49.341 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.81
RfactorNum. reflection% reflection
Rfree0.2446 2000 4.94 %
Rwork0.2187 --
obs0.22 40449 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 0 46 4098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024161
X-RAY DIFFRACTIONf_angle_d0.6065647
X-RAY DIFFRACTIONf_dihedral_angle_d26.9571529
X-RAY DIFFRACTIONf_chiral_restr0.047602
X-RAY DIFFRACTIONf_plane_restr0.003744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3981-2.45810.38751350.33222619X-RAY DIFFRACTION98
2.4581-2.52450.34011400.33032715X-RAY DIFFRACTION100
2.5245-2.59880.36161390.31912739X-RAY DIFFRACTION100
2.5988-2.68270.29231380.30422735X-RAY DIFFRACTION100
2.6827-2.77860.28951320.28792711X-RAY DIFFRACTION100
2.7786-2.88980.28771220.26952755X-RAY DIFFRACTION100
2.8898-3.02130.31791560.25442735X-RAY DIFFRACTION100
3.0213-3.18060.30171440.25132718X-RAY DIFFRACTION100
3.1806-3.37980.2491300.25372733X-RAY DIFFRACTION100
3.3798-3.64070.23421460.20882768X-RAY DIFFRACTION100
3.6407-4.00690.21131590.21162734X-RAY DIFFRACTION100
4.0069-4.58630.19221420.17952778X-RAY DIFFRACTION100
4.5863-5.77690.22051440.1752818X-RAY DIFFRACTION100
5.7769-49.35130.2441730.20062891X-RAY DIFFRACTION100
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)
10.1334-0.350.10811.95030.85840.7009-0.0436-0.048-0.0201-0.18730.1502-0.0203-0.10940.0067-00.4452-0.04530.01810.47210.01840.478-4.03-1.1254-38.4717
20.33270.1634-0.09491.87250.50240.6511-0.00760.12040.0949-0.05720.038-0.0417-0.13760.111700.4368-0.0657-0.00960.532-0.03890.4505-16.5388-50.6063-73.3795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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