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- PDB-9n5p: CRYSTAL STRUCTURE OF HUMAN IGG2 FC FRAGMENT-FC-GAMMA RECEPTOR IIA... -

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Basic information

Entry
Database: PDB / ID: 9n5p
TitleCRYSTAL STRUCTURE OF HUMAN IGG2 FC FRAGMENT-FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT
Components
  • Isoform 1 of Immunoglobulin heavy constant gamma 2
  • Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG2 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / FC GAMMA RECEPTOR IIA / CD32A
Function / homology
Function and homology information


IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex / FCGR3A-mediated IL10 synthesis / positive regulation of phagocytosis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation ...IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex / FCGR3A-mediated IL10 synthesis / positive regulation of phagocytosis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / adaptive immune response / cell surface receptor signaling pathway / external side of plasma membrane / Neutrophil degranulation / 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
Low affinity immunoglobulin gamma Fc region receptor II-a / Uncharacterized protein DKFZp686I04196
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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
DepositionFeb 4, 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

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Assembly

Deposited unit
A: Isoform 1 of Immunoglobulin heavy constant gamma 2
B: Isoform 1 of Immunoglobulin heavy constant gamma 2
C: Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5167
Polymers69,6363
Non-polymers3,8814
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint61 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.853, 66.949, 71.179
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-604-

HOH

21B-605-

HOH

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Isoform 1 of Immunoglobulin heavy constant gamma 2


Mass: 25112.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6N093
#2: Protein Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant / IgG Fc receptor II-a / CDw32 / Fc-gamma RII-a / Fc-gamma-RIIa / FcRII-a


Mass: 19410.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P12318

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Sugars , 3 types, 4 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}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: 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.: 1
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

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Non-polymers , 1 types, 281 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% PEG 2000 MME

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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: Jan 17, 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: 2→50 Å / Num. obs: 44826 / % possible obs: 89.5 % / Redundancy: 3.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.078 / Net I/σ(I): 28.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1928 / CC1/2: 0.634 / Rpim(I) all: 0.339 / % possible all: 77.2

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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: 2.01→27.55 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2222 4.96 %
Rwork0.1952 --
obs0.1971 44803 87.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 261 281 5270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065137
X-RAY DIFFRACTIONf_angle_d0.8487003
X-RAY DIFFRACTIONf_dihedral_angle_d19.5952142
X-RAY DIFFRACTIONf_chiral_restr0.053836
X-RAY DIFFRACTIONf_plane_restr0.006871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.050.3175970.26561741X-RAY DIFFRACTION57
2.05-2.10.3311320.26372340X-RAY DIFFRACTION78
2.1-2.150.29791150.26982415X-RAY DIFFRACTION80
2.15-2.210.29351450.24852503X-RAY DIFFRACTION84
2.21-2.270.29391390.25182592X-RAY DIFFRACTION86
2.27-2.350.30341400.25442725X-RAY DIFFRACTION90
2.35-2.430.2231340.23552722X-RAY DIFFRACTION89
2.43-2.530.35591210.24552441X-RAY DIFFRACTION81
2.53-2.640.32221430.23942819X-RAY DIFFRACTION93
2.64-2.780.28491550.23022929X-RAY DIFFRACTION97
2.78-2.950.29691530.22212946X-RAY DIFFRACTION97
2.95-3.180.22491490.22372945X-RAY DIFFRACTION97
3.18-3.50.23631460.19072958X-RAY DIFFRACTION97
3.5-4.010.19561490.17452881X-RAY DIFFRACTION94
4.01-5.040.16861540.1482521X-RAY DIFFRACTION83
5.04-27.550.21461500.16293103X-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)
11.5316-0.09840.01050.815-0.22760.7389-0.10470.31180.10320.00570.0626-0.00820.10620.19760.01330.3048-0.0783-0.02330.37170.00370.323641.051231.4671-18.0836
20.81310.44660.02430.4597-0.51910.73640.01820.20460.14570.082-0.09670.18350.04960.2239-0.07730.3222-0.0286-0.01520.41370.04840.361713.473826.8596-24.7323
30.9150.3-0.88880.0095-0.03060.8426-0.0968-0.1033-0.01430.01080.0058-0.030.10230.1105-00.41010.08530.02970.32960.04650.340814.34575.007818.3221
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 1 through 171)

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