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- PDB-7uru: Crystal structure of the low affinity Fc gamma receptor IIIA vari... -

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Basic information

Entry
Database: PDB / ID: 7uru
TitleCrystal structure of the low affinity Fc gamma receptor IIIA variant in complex with the Fc of IgG1.
Components
  • Immunoglobulin gamma-1 heavy chain
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / RECEPTOR COMPLEX / FC RECEPTOR / ANTIBODY / IGG1 / CD16
Function / homology
Function and homology information


low-affinity IgG receptor activity / immune receptor activity / natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / positive regulation of natural killer cell proliferation / natural killer cell activation / antibody-dependent cellular cytotoxicity ...low-affinity IgG receptor activity / immune receptor activity / natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / positive regulation of natural killer cell proliferation / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / natural killer cell mediated cytotoxicity / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / FCGR3A-mediated IL10 synthesis / FCGR3A-mediated phagocytosis / calcium-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...: / Immunoglobulin domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor III-A / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI162242 United States
CitationJournal: To Be Published
Title: Crystal structure of the low affinity Fc gamma receptor IIIA variant in complex with the Fc of IgG1.
Authors: Tolbert, W.D. / Pazgier, M.
History
DepositionApr 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
C: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8277
Polymers70,4573
Non-polymers3,3694
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.983, 100.750, 124.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 25097.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Protein Low affinity immunoglobulin gamma Fc region receptor III-A / IgG Fc receptor III-A / CD16-II / CD16a antigen / Fc-gamma RIII-alpha / Fc-gamma RIII / Fc-gamma ...IgG Fc receptor III-A / CD16-II / CD16a antigen / Fc-gamma RIII-alpha / Fc-gamma RIII / Fc-gamma RIIIa / FcRIII / FcRIIIa / FcgammaRIIIA / FcR-10 / IgG Fc receptor III-2


Mass: 20262.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR3A, CD16A, FCG3, FCGR3, IGFR3 / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: P08637
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#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.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 8% PEG 8000 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2022
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35352 / % possible obs: 96 % / Redundancy: 5.5 % / CC1/2: 0.941 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.077 / Net I/σ(I): 26.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1636 / CC1/2: 0.47 / Rpim(I) all: 0.655 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGJ

3sgj


Resolution: 2.4→32.43 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 1734 4.91 %
Rwork0.2152 --
obs0.2176 35299 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 226 14 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125136
X-RAY DIFFRACTIONf_angle_d1.3096991
X-RAY DIFFRACTIONf_dihedral_angle_d6.228775
X-RAY DIFFRACTIONf_chiral_restr0.067822
X-RAY DIFFRACTIONf_plane_restr0.009867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.42681040.40442174X-RAY DIFFRACTION74
2.46-2.540.42471340.36562624X-RAY DIFFRACTION90
2.54-2.630.40331340.3392646X-RAY DIFFRACTION91
2.63-2.730.39821510.34712689X-RAY DIFFRACTION93
2.73-2.860.39951550.32162711X-RAY DIFFRACTION94
2.86-3.010.34881430.2952880X-RAY DIFFRACTION98
3.01-3.20.31581470.26532938X-RAY DIFFRACTION99
3.2-3.440.29561360.23632956X-RAY DIFFRACTION100
3.44-3.790.26411780.21232864X-RAY DIFFRACTION99
3.79-4.340.23131420.18662996X-RAY DIFFRACTION100
4.34-5.460.19991400.16092986X-RAY DIFFRACTION99
5.46-32.430.22051700.1843101X-RAY DIFFRACTION99
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)
11.4307-0.99271.38093.4474-1.8327.1710.1195-0.00730.00170.3084-0.1441-0.04790.31310.11340.0040.4257-0.01540.09620.4676-0.11880.5018-0.0087-37.22098.9248
21.3106-0.394-0.72561.990.94389.20720.2138-0.0306-0.316-0.0178-0.14650.04380.3994-0.6697-0.06440.3525-0.0189-0.11860.41490.00810.5565-19.4842-16.432311.0052
33.4266-1.445-2.70543.71413.07245.3591-0.1998-0.3369-0.03610.50560.2481-0.18230.97520.1647-0.04380.7979-0.003-0.11390.36890.05030.4653-2.5726-17.288157.4915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 233 through 444)
2X-RAY DIFFRACTION2(chain 'B' and resid 232 through 444)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 175)

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