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- PDB-9ouv: Crystal structure of human IGG1 FC fragment-FC-gamma receptor IIB... -

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Basic information

Entry
Database: PDB / ID: 9ouv
TitleCrystal structure of human IGG1 FC fragment-FC-gamma receptor IIB complex
Components
  • Immunoglobulin gamma-1 heavy chain Fc fragment
  • Low affinity immunoglobulin gamma Fc region receptor II-b
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / FC GAMMA RECEPTOR IIB / CD32B
Function / homology
Function and homology information


negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of dendritic cell antigen processing and presentation ...negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of dendritic cell antigen processing and presentation / positive regulation of humoral immune response / negative regulation of humoral immune response mediated by circulating immunoglobulin / low-affinity IgG receptor activity / negative regulation of immunoglobulin production / negative regulation of acute inflammatory response to antigenic stimulus / negative regulation of B cell activation / negative regulation of cytotoxic T cell degranulation / negative regulation of dendritic cell differentiation / negative regulation of B cell receptor signaling pathway / regulation of dendritic spine maintenance / negative regulation of macrophage activation / IgG receptor activity / mature B cell differentiation involved in immune response / follicular B cell differentiation / regulation of adaptive immune response / cellular response to molecule of bacterial origin / negative regulation of immune response / Fc-gamma receptor signaling pathway / negative regulation of neutrophil activation / antibody-dependent cellular cytotoxicity / IgG binding / negative regulation of phagocytosis / negative regulation of cytokine production / phagocytosis, engulfment / regulation of innate immune response / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / immunoglobulin mediated immune response / immunoglobulin complex / phagocytosis / receptor-mediated endocytosis / positive regulation of phagocytosis / cerebellum development / positive regulation of JNK cascade / response to bacterium / defense response / antigen processing and presentation of exogenous peptide antigen via MHC class II / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / amyloid-beta binding / cell body / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / external side of plasma membrane / protein-containing complex binding / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...: / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Low affinity immunoglobulin gamma Fc region receptor II-b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 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: Front Immunol / Year: 2025
Title: Cross-species analysis of FcgRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque
Authors: Tolbert, W.D. / Nhan, P.B. / Conley, H.E. / Ge, X. / Chandravanshi, M. / Lee, M. / Veilleux, J. / Korzeniowski, M. / Gottumukkala, S. / Ackerman, M.E. / Pollara, J. / Pazgier, M.
History
DepositionMay 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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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 Fc fragment
B: Immunoglobulin gamma-1 heavy chain Fc fragment
C: Low affinity immunoglobulin gamma Fc region receptor II-b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4157
Polymers69,6403
Non-polymers3,7764
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint63 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.385, 76.086, 120.718
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Immunoglobulin gamma-1 heavy chain Fc fragment / 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 line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Protein Low affinity immunoglobulin gamma Fc region receptor II-b / IgG Fc receptor II-b / CDw32 / Fc-gamma RII-b / Fc-gamma-RIIb / FcRII-b


Mass: 19444.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2B, CD32, FCG2, IGFR2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P31994
#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 150 mM sodium chloride 100 mM Tris-HCl pH 8.0 8% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 16, 2025
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.07→50 Å / Num. obs: 16276 / % possible obs: 95.9 % / Redundancy: 3.4 % / CC1/2: 0.95 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.094 / Net I/σ(I): 9.9
Reflection shellResolution: 3.07→3.12 Å / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 710 / CC1/2: 0.48 / Rpim(I) all: 0.574 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→32.63 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 723 4.94 %
Rwork0.1859 --
obs0.1886 14638 87.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.07→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 254 1 5045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045181
X-RAY DIFFRACTIONf_angle_d0.7937066
X-RAY DIFFRACTIONf_dihedral_angle_d17.3852150
X-RAY DIFFRACTIONf_chiral_restr0.062841
X-RAY DIFFRACTIONf_plane_restr0.007880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.310.2842740.26631709X-RAY DIFFRACTION53
3.31-3.640.31131260.23122725X-RAY DIFFRACTION85
3.64-4.170.2621810.19563112X-RAY DIFFRACTION98
4.17-5.240.20571650.15863166X-RAY DIFFRACTION99
5.24-32.630.22511770.17223203X-RAY DIFFRACTION98
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)
10.57710.3190.03560.40040.0320.2592-0.08890.1647-0.30010.02160.14250.00510.2237-0.02770.12460.16980.05140.06140.1129-0.04760.2756-28.7888-11.1625-50.0909
20.62660.2221-0.22710.5489-0.21370.2403-0.22750.08370.67830.0720.2405-0.4355-0.3131-0.01180.13230.13510.06740.0117-0.06250.09850.0982-9.32179.5712-49.3059
30.08020.0072-0.10060.1632-0.0680.12260.4749-0.1069-0.13210.5298-0.25930.08550.08830.09720.07770.66450.0505-0.22520.70060.06690.23380.1207-11.0683-7.5493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 231 through 445)
2X-RAY DIFFRACTION2(chain 'B' and resid 231 through 445)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 173)

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