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- PDB-6nk3: Crystal structure of murine Mxra8 ectodomain -

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Basic information

Entry
Database: PDB / ID: 6nk3
TitleCrystal structure of murine Mxra8 ectodomain
ComponentsMatrix remodeling-associated protein 8
KeywordsCELL INVASION / Chikungunya / virus receptor / Immunoglobulin-like / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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: 2.2 Å
AuthorsFremont, D.H. / Kim, A.S. / Nelson, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

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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)62,3342
Polymers62,3342
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-7 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.550, 142.700, 195.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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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: 31166.775 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 23-296)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mxra8, Asp3, Dicam / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DBV4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 8% PEG8000, 25% ethylene glycol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 5, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.2→48.46 Å / Num. obs: 51479 / % possible obs: 99.42 % / Redundancy: 26.4 % / Biso Wilson estimate: 51.15 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.63
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 17.7 % / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4856 / CC1/2: 0.666 / % possible all: 95.83

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
PDB_EXTRACT3.24data extraction
XDSJan 26, 2018data reduction
Aimless0.6.3data scaling
PHENIX1.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MJ6

3mj6


Resolution: 2.2→48.46 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2258 1577 3.08 %
Rwork0.1988 --
obs0.1997 51265 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.52 Å2 / Biso mean: 70 Å2 / Biso min: 26.67 Å2
Refinement stepCycle: final / Resolution: 2.2→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 0 266 4524
Biso mean---72.62 -
Num. residues----528
Refinement TLS params.Method: refined / Origin x: 62.4581 Å / Origin y: 25.9824 Å / Origin z: 55.8634 Å
111213212223313233
T0.3954 Å20.0762 Å2-0.0189 Å2-0.3669 Å2-0.026 Å2--0.3265 Å2
L0.0568 °2-0.1995 °2-0.1973 °2-2.052 °21.4625 °2--0.8511 °2
S-0.0772 Å °-0.0837 Å °-0.0161 Å °0.0464 Å °0.1004 Å °-0.0214 Å °0.05 Å °0.0334 Å °0.003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 294
2X-RAY DIFFRACTION1allB30 - 294
3X-RAY DIFFRACTION1allS22 - 190
4X-RAY DIFFRACTION1allS191
5X-RAY DIFFRACTION1allS192 - 234
6X-RAY DIFFRACTION1allS235 - 247
7X-RAY DIFFRACTION1allS248 - 259
8X-RAY DIFFRACTION1allS260 - 291
9X-RAY DIFFRACTION1allS292 - 302

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