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- PDB-9oc6: Crystal structure of receptor FcRn bound to Human Astrovirus 6 spike -

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Basic information

Entry
Database: PDB / ID: 9oc6
TitleCrystal structure of receptor FcRn bound to Human Astrovirus 6 spike
Components
  • Beta-2-microglobulin
  • Capsid polyprotein VP90
  • IgG receptor FcRn large subunit p51
KeywordsIMMUNE SYSTEM / Astrovirus / FcRn / virus host interaction / HAstV
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / T=3 icosahedral viral capsid / IgG binding / beta-2-microglobulin binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / T=3 icosahedral viral capsid / IgG binding / beta-2-microglobulin binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / host extracellular space / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Capsid polyprotein VP90 / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human astrovirus 6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsAgrawal, S. / Wilson, I.A.
CitationJournal: Cell Rep / Year: 2025
Title: Structural Hijacking of FcRn by Human Astrovirus Spikes Reveals Conserved Epitopes for Broad-Spectrum Antivirals
Authors: Agrawal, S. / Jain, M. / Marinelli, D. / Briney, B. / Wilson, I.A.
History
DepositionApr 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
A: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)70,0863
Polymers70,0863
Non-polymers00
Water00
1
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
A: Capsid polyprotein VP90

C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
A: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)140,1716
Polymers140,1716
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)211.925, 76.682, 53.807
Angle α, β, γ (deg.)90.000, 98.552, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 30408.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Homo sapiens (human) / References: UniProt: P55899
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / References: UniProt: P61769
#3: Protein Capsid polyprotein VP90


Mass: 27929.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus 6 / Gene: ORF2 / Production host: Homo sapiens (human) / References: UniProt: A0A3G6VE58
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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 30% 1,2-propanediol, 20% PEG-400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.97→29.14 Å / Num. obs: 17653 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 63.51 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.152 / Net I/σ(I): 10.7
Reflection shellResolution: 2.97→3.05 Å / Rmerge(I) obs: 0.821 / Num. unique obs: 1254 / CC1/2: 0.726

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
FAST_DPdata reduction
FAST_DPdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→29.14 Å / SU ML: 0.4179 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.3965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 1765 10 %
Rwork0.2279 15880 -
obs0.2331 17645 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.18 Å2
Refinement stepCycle: LAST / Resolution: 2.97→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 0 0 4351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244473
X-RAY DIFFRACTIONf_angle_d0.53316085
X-RAY DIFFRACTIONf_chiral_restr0.041654
X-RAY DIFFRACTIONf_plane_restr0.0043781
X-RAY DIFFRACTIONf_dihedral_angle_d19.18441617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.050.36921300.30131164X-RAY DIFFRACTION96.64
3.05-3.140.3291360.27681235X-RAY DIFFRACTION99.93
3.14-3.240.32141330.24031188X-RAY DIFFRACTION99.7
3.24-3.360.27761380.23281242X-RAY DIFFRACTION99.78
3.36-3.490.24141320.22521192X-RAY DIFFRACTION99.92
3.5-3.650.29341370.22641227X-RAY DIFFRACTION99.93
3.65-3.850.28341360.22841227X-RAY DIFFRACTION100
3.85-4.090.28421360.21671219X-RAY DIFFRACTION100
4.09-4.40.27271350.20411217X-RAY DIFFRACTION99.93
4.4-4.840.26011370.20541237X-RAY DIFFRACTION99.93
4.84-5.540.25861360.22111220X-RAY DIFFRACTION99.85
5.54-6.960.26551380.25311246X-RAY DIFFRACTION100
6.96-29.140.29261410.22581266X-RAY DIFFRACTION99.72

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