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

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Basic information

Entry
Database: PDB / ID: 8dir
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 / Resolution: 2.3 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 29, 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 1.2Oct 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
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)83,9198
Polymers80,5993
Non-polymers3,3205
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint20 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.286, 89.276, 56.032
Angle α, β, γ (deg.)90.000, 97.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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
#3: 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.: 2
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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Sodium Formate (pH6.6)

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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: 2.3→50 Å / Num. obs: 44290 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 43.45 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.3
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2235

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Processing

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

4x4m


Resolution: 2.3→36.87 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2187 4.95 %
Rwork0.1962 42026 -
obs0.198 44213 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.25 Å2 / Biso mean: 61.7028 Å2 / Biso min: 20.93 Å2
Refinement stepCycle: final / Resolution: 2.3→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5492 0 223 244 5959
Biso mean--72.58 47.25 -
Num. residues----692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.350.36541200.30762570269097
2.35-2.40.35691340.26926102744100
2.4-2.460.2871480.25262617276599
2.46-2.530.28661160.22132601271799
2.53-2.610.29521330.23292590272399
2.61-2.690.26251420.222526372779100
2.69-2.790.27321260.228726402766100
2.79-2.90.29091270.246126212748100
2.9-3.030.28681370.263426302767100
3.03-3.190.2361410.220926422783100
3.19-3.390.2471530.205126032756100
3.39-3.650.25171300.201226432773100
3.65-4.020.22121560.179526242780100
4.02-4.60.20791430.154126282771100
4.6-5.790.15961390.149526632802100
5.79-36.870.19811420.17052707284999
Refinement TLS params.Method: refined / Origin x: 34.4459 Å / Origin y: -47.1638 Å / Origin z: 35.6579 Å
111213212223313233
T0.2318 Å2-0.011 Å20.0077 Å2-0.2252 Å2-0.0427 Å2--0.2535 Å2
L0.416 °2-0.2927 °20.3072 °2-0.5785 °2-0.4093 °2--0.7824 °2
S-0.0058 Å °0.018 Å °0.0321 Å °0.0061 Å °0.0268 Å °-0.0194 Å °0.0891 Å °-0.0076 Å °-0.0296 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB231 - 509
2X-RAY DIFFRACTION1allA232 - 509
3X-RAY DIFFRACTION1allA601
4X-RAY DIFFRACTION1allC19 - 280
5X-RAY DIFFRACTION1allC301 - 401
6X-RAY DIFFRACTION1allS1 - 269

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