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- PDB-9mcy: CRYSTAL STRUCTURE OF HUMAN IGG1 FC FRAGMENT-FC-GAMMA RECEPTOR IIA... -

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Basic information

Entry
Database: PDB / ID: 9mcy
TitleCRYSTAL STRUCTURE OF HUMAN IGG1 FC FRAGMENT-FC-GAMMA RECEPTOR IIA COMPLEX R131 VARIANT
Components
  • Fc gamma receptor IIA R131 variant
  • Immunoglobulin gamma-1 heavy chain Fc fragment
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / FC GAMMA RECEPTOR IIA / CD32A
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / 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
Fc gamma receptor RIIa3 splice variant / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
DepositionDec 5, 2024Deposition 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
E: Fc gamma receptor IIA R131 variant
C: Immunoglobulin gamma-1 heavy chain Fc fragment
D: Immunoglobulin gamma-1 heavy chain Fc fragment
F: Fc gamma receptor IIA R131 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,20615
Polymers139,2496
Non-polymers6,9579
Water19811
1
A: Immunoglobulin gamma-1 heavy chain Fc fragment
B: Immunoglobulin gamma-1 heavy chain Fc fragment
E: Fc gamma receptor IIA R131 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1977
Polymers69,6253
Non-polymers3,5724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint42 kcal/mol
Surface area30490 Å2
MethodPISA
2
C: Immunoglobulin gamma-1 heavy chain Fc fragment
D: Immunoglobulin gamma-1 heavy chain Fc fragment
F: Fc gamma receptor IIA R131 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0098
Polymers69,6253
Non-polymers3,3845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint28 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.993, 76.229, 120.046
Angle α, β, γ (deg.)96.60, 100.24, 90.08
Int Tables number1
Space group name H-MP1

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Components

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Antibody / Protein , 2 types, 6 molecules ABCDEF

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


Mass: 25097.434 Da / Num. of mol.: 4
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 Fc gamma receptor IIA R131 variant


Mass: 19429.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2A / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A346JF56

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Sugars , 3 types, 7 molecules

#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.: 1
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.: 4
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.: 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

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Non-polymers , 2 types, 13 molecules

#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 5000 MME, 12% isopropanol , 0.1 M MES pH 6.5

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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: Aug 2, 2024
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 38384 / % possible obs: 95.6 % / Redundancy: 3.2 % / CC1/2: 0.76 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.112 / Net I/σ(I): 12.5
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1406 / CC1/2: 0.64 / Rpim(I) all: 0.478 / % possible all: 70.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→39.89 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 1902 4.96 %
Rwork0.1766 --
obs0.1796 38370 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9504 0 468 11 9983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110278
X-RAY DIFFRACTIONf_angle_d1.18214027
X-RAY DIFFRACTIONf_dihedral_angle_d8.5771550
X-RAY DIFFRACTIONf_chiral_restr0.0691661
X-RAY DIFFRACTIONf_plane_restr0.011754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.890.3163670.25081506X-RAY DIFFRACTION54
2.89-2.970.28191350.26582420X-RAY DIFFRACTION89
2.97-3.060.34291550.26022714X-RAY DIFFRACTION96
3.06-3.160.31231280.23112652X-RAY DIFFRACTION97
3.16-3.270.25911410.2132766X-RAY DIFFRACTION98
3.27-3.40.29161410.19792636X-RAY DIFFRACTION98
3.4-3.550.26551430.19852747X-RAY DIFFRACTION98
3.55-3.740.28691600.19712744X-RAY DIFFRACTION98
3.74-3.980.24541390.17162675X-RAY DIFFRACTION98
3.98-4.280.21761210.15812650X-RAY DIFFRACTION94
4.28-4.710.18221500.13552721X-RAY DIFFRACTION99
4.71-5.390.17391610.13652795X-RAY DIFFRACTION100
5.39-6.790.25211240.17862730X-RAY DIFFRACTION99
6.79-39.890.19981370.15822712X-RAY DIFFRACTION97
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)
10.0361-0.19540.10170.23280.00950.0816-0.0332-0.0205-0.00740.0029-0.00520.0279-0.0192-0.00900.1555-0.022-0.02420.17410.00770.1701-17.3175-26.156616.9157
2-0.33750.1114-0.26180.3037-0.02750.0529-0.1199-0.0846-0.1961-0.03710.0756-0.0106-0.0396-0.0183-00.1487-0.04030.00550.1663-0.03290.25671.774-46.991116.5872
30.06760.0087-0.00790.1188-0.06580.0945-0.1198-0.17810.1673-0.39450.07030.10270.09450.026-00.8033-0.04030.06690.6548-0.04610.421212.3082-27.536-25.2264
40.19380.11740.16220.12080.00760.0979-0.01830.01610.0847-0.01530.00370.01690.0657-0.0413-00.1340.02640.01490.14580.00850.17314.11854.4187-79.9625
5-0.08380.15590.10710.2379-0.07520.1618-0.04770.06110.12270.01770.03620.00840.01440.033100.17690.0390.0040.1789-0.01810.259523.287725.1816-79.8587
6-0.01430.0490.0570.1075-0.0780.01510.13640.198-0.09140.5558-0.32240.0147-0.0351-0.0624-00.7902-0.0661-0.12220.53680.06010.337733.11045.6647-38.9732
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 444)
3X-RAY DIFFRACTION3(chain 'E' and resid 1 through 172)
4X-RAY DIFFRACTION4(chain 'C' and resid 231 through 445)
5X-RAY DIFFRACTION5(chain 'D' and resid 231 through 444)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 173)

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