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- PDB-3d5o: Structural recognition and functional activation of FcrR by innat... -

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Basic information

Entry
Database: PDB / ID: 3d5o
TitleStructural recognition and functional activation of FcrR by innate pentraxins
Components
  • Low affinity immunoglobulin gamma Fc region receptor II-a
  • Serum amyloid P-component
KeywordsIMMUNE SYSTEM / complex structure / SAP / Fc RIIa / Fc receptor activation / pentraxins / Amyloid / Glycoprotein / Lectin / Metal-binding / Secreted / Cell membrane / IgG-binding protein / Immunoglobulin domain / Membrane / Phosphoprotein / Receptor / Transmembrane
Function / homology
Function and homology information


negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / IgG receptor activity / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell ...negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / IgG receptor activity / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell / virion binding / antibody-dependent cellular cytotoxicity / IgG binding / negative regulation of acute inflammatory response / FCGR activation / chaperone-mediated protein complex assembly / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / acute-phase response / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / unfolded protein binding / protein folding / carbohydrate binding / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / Amyloid fiber formation / external side of plasma membrane / innate immune response / calcium ion binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / : / Immunoglobulin domain / Jelly Rolls - #200 ...: / Pentaxin, conserved site / Pentraxin domain signature. / Pentaxin family / Pentraxin / C-reactive protein / pentaxin family / Pentraxin-related / Pentraxin (PTX) domain profile. / : / Immunoglobulin domain / Jelly Rolls - #200 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serum amyloid P-component / Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLu, J. / Marnell, L.L. / Marjon, K.D. / Mold, C. / Du Clos, T.W. / Sun, P.D.
CitationJournal: Nature / Year: 2008
Title: Structural recognition and functional activation of FcgammaR by innate pentraxins.
Authors: Lu, J. / Marnell, L.L. / Marjon, K.D. / Mold, C. / Du Clos, T.W. / Sun, P.D.
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum amyloid P-component
B: Serum amyloid P-component
C: Serum amyloid P-component
D: Serum amyloid P-component
E: Serum amyloid P-component
F: Low affinity immunoglobulin gamma Fc region receptor II-a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,22228
Polymers136,4876
Non-polymers2,73522
Water55831
1
F: Low affinity immunoglobulin gamma Fc region receptor II-a
hetero molecules

D: Serum amyloid P-component
hetero molecules

A: Serum amyloid P-component
B: Serum amyloid P-component
C: Serum amyloid P-component
E: Serum amyloid P-component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,22228
Polymers136,4876
Non-polymers2,73522
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-243 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.197, 143.477, 161.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
Serum amyloid P-component / SAP / 9.5S alpha-1-glycoprotein / Serum amyloid P-component(1-203)


Mass: 23282.455 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02743
#2: Protein Low affinity immunoglobulin gamma Fc region receptor II-a / IgG Fc receptor II-a / Fc-gamma RII-a / Fc-gamma-RIIa / FcRII-a / CDw32


Mass: 20074.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P12318

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Sugars , 1 types, 5 molecules

#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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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Non-polymers , 3 types, 48 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsAUTHORS STATE THAT CHAIN F IS THE ECTODOMAIN OF FC GAMMA RECEPTOR IIA, WHICH HAS A POLYMORPHISM AT ...AUTHORS STATE THAT CHAIN F IS THE ECTODOMAIN OF FC GAMMA RECEPTOR IIA, WHICH HAS A POLYMORPHISM AT THIS POSITION, E.G. R131 IN THIS STRUCTURE AND H167 IN SEQUENCE DATABASE.

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0 M NH4SO4, 5% iso-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 37599 / Num. obs: 36697 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 68.7 Å2 / Rsym value: 0.091
Reflection shellResolution: 2.8→2.87 Å / % possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 1401 Random
Rwork0.207 --
all0.248 37585 -
obs0.221 35208 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9468 0 156 31 9655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3676 102 -
Rwork0.2999 --
obs-2646 0.748 %

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