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- PDB-8dj7: The complex structure between human IgG1 Fc and its high affinity... -

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Basic information

Entry
Database: PDB / ID: 8dj7
TitleThe complex structure between human IgG1 Fc and its high affinity receptor FcgRI H174R variant
Components
  • High affinity immunoglobulin gamma Fc receptor I
  • Ig gamma-1 Fc chain
KeywordsIMMUNE SYSTEM / High affinity IgG1 Fc receptor
Function / homology
Function and homology information


high-affinity IgG receptor activity / IgG receptor activity / phagocytosis, recognition / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / positive regulation of type IIa hypersensitivity / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity ...high-affinity IgG receptor activity / IgG receptor activity / phagocytosis, recognition / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / positive regulation of type IIa hypersensitivity / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / immunoglobulin receptor binding / Cross-presentation of soluble exogenous antigens (endosomes) / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / phagocytosis, engulfment / antigen processing and presentation of exogenous peptide antigen via MHC class I / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / receptor-mediated endocytosis / FCGR3A-mediated IL10 synthesis / positive regulation of phagocytosis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / antibacterial humoral response / early endosome membrane / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / cell surface receptor signaling pathway / defense response to bacterium / immune response / innate immune response / external side of plasma membrane / signal transduction / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Immunoglobulin heavy constant gamma 1 / High affinity immunoglobulin gamma Fc receptor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsLu, J. / Sun, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Division of ntramural research United States
CitationJournal: Front Immunol / Year: 2023
Title: Fc gamma RI FG-loop functions as a pH sensitive switch for IgG binding and release.
Authors: Lu, J. / Spencer, M. / Zou, Z. / Traver, M. / Brzostowski, J. / Sun, P.D.
History
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 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 1.2Nov 13, 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
B: Ig gamma-1 Fc chain
A: Ig gamma-1 Fc chain
C: High affinity immunoglobulin gamma Fc receptor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8807
Polymers80,5993
Non-polymers3,2814
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint30 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.371, 89.037, 56.191
Angle α, β, γ (deg.)90.000, 96.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 3 molecules BAC

#1: Protein Ig gamma-1 Fc chain / IgG1 Fc


Mass: 24698.955 Da / Num. of mol.: 2 / Fragment: CH2 and CH3 regions, residues 112-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: Protein High affinity immunoglobulin gamma Fc receptor I / IgG Fc receptor I / Fc-gamma RI / FcRI / Fc-gamma RIA / FcgammaRIa


Mass: 31201.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR1A, FCG1, FCGR1, IGFR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12314

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Sugars , 2 types, 2 molecules

#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.: 1
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: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 124 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Magnesium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 37909 / % possible obs: 96.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 51.03 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.3
Reflection shellResolution: 2.39→2.46 Å / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1953

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x4m

4x4m


Resolution: 2.39→37.17 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1834 4.85 %
Rwork0.2141 35956 -
obs0.2166 37790 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.04 Å2 / Biso mean: 69.657 Å2 / Biso min: 26.3 Å2
Refinement stepCycle: final / Resolution: 2.39→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5319 0 219 122 5660
Biso mean--78.94 52.95 -
Num. residues----669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.460.36041390.34062382252183
2.46-2.530.33371410.27172851299299
2.53-2.610.32341520.2652912306499
2.61-2.710.33531580.23982883304199
2.71-2.810.3021350.24072895303099
2.81-2.940.32481330.25962874300798
2.94-3.10.33761210.27332892301399
3.1-3.290.3391330.22652851298497
3.29-3.550.24861350.21582685282092
3.55-3.90.24961580.20092840299898
3.9-4.470.22051360.18232685282191
4.47-5.620.20631570.17772493265085
5.62-37.170.26281360.19792713284991
Refinement TLS params.Method: refined / Origin x: 37.5998 Å / Origin y: -48.1481 Å / Origin z: 7.4835 Å
111213212223313233
T0.3176 Å2-0.0271 Å20.0449 Å2-0.2896 Å2-0.0298 Å2--0.327 Å2
L0.5233 °2-0.4537 °20.507 °2-1.0388 °2-0.5872 °2--1.0448 °2
S-0.0329 Å °-0.036 Å °0.0325 Å °0.0678 Å °0.101 Å °0.0581 Å °0.0485 Å °-0.0625 Å °-0.0557 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB231 - 508
2X-RAY DIFFRACTION1allA232 - 509
3X-RAY DIFFRACTION1allC19 - 273
4X-RAY DIFFRACTION1allS2 - 133
5X-RAY DIFFRACTION1allD1 - 2

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