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- PDB-1ovz: Crystal structure of human FcaRI -

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Basic information

Entry
Database: PDB / ID: 1ovz
TitleCrystal structure of human FcaRI
ComponentsImmunoglobulin alpha Fc receptor
KeywordsIMMUNE SYSTEM / FcaRI / CD89 / IgA / Fc receptor / immunoglobulin-like domain
Function / homology
Function and homology information


IgA receptor activity / cellular response to interferon-alpha / Fc receptor signaling pathway / immune response-regulating signaling pathway / IgA binding / positive regulation of neutrophil apoptotic process / neutrophil activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / cellular response to interleukin-6 / neutrophil mediated immunity ...IgA receptor activity / cellular response to interferon-alpha / Fc receptor signaling pathway / immune response-regulating signaling pathway / IgA binding / positive regulation of neutrophil apoptotic process / neutrophil activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / cellular response to interleukin-6 / neutrophil mediated immunity / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / cellular response to type II interferon / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / immune response / Neutrophil degranulation / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin alpha Fc receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsHerr, A.B. / Ballister, E.R. / Bjorkman, P.J.
Citation
Journal: Nature / Year: 2003
Title: Insights into IgA-mediated immune responses from the crystal structures of human Fc-alpha-RI and its complex with IgA1-Fc
Authors: Herr, A.B. / Ballister, E.R. / Bjorkman, P.J.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Bivalent Binding of IgA1 to FcaRI Suggests a Mechanism for Cytokine Activation of IgA Phagocytosis
Authors: Herr, A.B. / White, C.L. / Milburn, C. / Wu, C. / Bjorkman, P.J.
History
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 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 / _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: Immunoglobulin alpha Fc receptor
B: Immunoglobulin alpha Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4427
Polymers47,2312
Non-polymers1,2105
Water00
1
A: Immunoglobulin alpha Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3834
Polymers23,6161
Non-polymers7683
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin alpha Fc receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0583
Polymers23,6161
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.150, 158.150, 39.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsThe biological assembly state is a monomer.

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Components

#1: Protein Immunoglobulin alpha Fc receptor / IgA Fc receptor / CD89 antigen


Mass: 23615.742 Da / Num. of mol.: 2 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCAR OR CD89 / Plasmid: pAcGP67 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High 5 insect cells / References: UniProt: P24071
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


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


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
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: 2.36 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
20.1 MMES1reservoirpH6.0
320 %PEG60001drop
40.1 Msodium phosphate1droppH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2001
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 10246 / Num. obs: 10204 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.4
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.9 / Num. unique all: 517 / % possible all: 100
Reflection
*PLUS
Num. obs: 10246 / % possible obs: 99.7 % / Num. measured all: 154491
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3→24.79 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 991 10.3 %RANDOM
Rwork0.235 ---
all0.235 10204 --
obs0.235 9590 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5159 Å2 / ksol: 0.335763 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--11.65 Å20 Å20 Å2
2---11.65 Å20 Å2
3---23.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 78 0 2884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d1.08
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.406 78 10.4 %
Rwork0.326 672 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3TRIS.PARTRIS.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.291
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
X-RAY DIFFRACTIONc_angle_deg1.43

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