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

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Basic information

Entry
Database: PDB / ID: 9mcx
TitleCRYSTAL STRUCTURE OF HUMAN IGG1 FC FRAGMENT-FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT
Components
  • Immunoglobulin gamma-1 heavy chain Fc fragment
  • Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / 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
Immunoglobulin gamma-1 heavy chain / Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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

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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-a H131 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4867
Polymers69,6063
Non-polymers3,8814
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint62 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.122, 66.104, 72.094
Angle α, β, γ (deg.)90.00, 94.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody / Protein / Non-polymers , 3 types, 219 molecules ABC

#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-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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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-Glycam 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
[]{[(4+1)][b-D-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-Glycam 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
[]{[(4+1)][b-D-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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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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 2000 MME, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 15, 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: 2.38→50 Å / Num. obs: 28466 / % possible obs: 93.5 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.042 / Net I/σ(I): 43.9
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1413 / CC1/2: 0.95 / Rpim(I) all: 0.139 / % possible all: 93.5

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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: 2.38→28.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 1306 4.87 %
Rwork0.1845 --
obs0.187 26814 88.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 261 216 5209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055138
X-RAY DIFFRACTIONf_angle_d0.8127007
X-RAY DIFFRACTIONf_dihedral_angle_d6.499793
X-RAY DIFFRACTIONf_chiral_restr0.052840
X-RAY DIFFRACTIONf_plane_restr0.008869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.480.34351190.24922285X-RAY DIFFRACTION71
2.48-2.590.30241240.23342506X-RAY DIFFRACTION79
2.59-2.730.31261400.2292808X-RAY DIFFRACTION88
2.73-2.90.26341390.22752965X-RAY DIFFRACTION92
2.9-3.120.2991420.2242699X-RAY DIFFRACTION84
3.12-3.430.23541770.19463050X-RAY DIFFRACTION96
3.43-3.930.20831480.17793142X-RAY DIFFRACTION97
3.93-4.950.20261680.1423080X-RAY DIFFRACTION95
4.95-28.020.18861490.15862973X-RAY DIFFRACTION90
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)
11.5546-0.17370.14830.7203-0.4281.1437-0.06270.20430.03680.05030.00150.01050.0070.05450.05710.2417-0.051-0.00630.2301-0.03290.220738.144132.646317.7528
20.87740.6231-0.3280.8635-0.29520.78940.00410.20710.1872-0.041-0.00160.1907-0.0210.05690.01060.2225-0.0044-0.03130.30.03150.269410.911627.977710.9784
31.56280.2897-0.84910.56380.16730.971-0.0971-0.1381-0.2110.1042-0.0226-0.06570.18190.0150.09880.28210.06790.01130.20220.04480.239111.43596.518954.5631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 234 through 444)
2X-RAY DIFFRACTION2(chain 'B' and resid 233 through 444)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 171)

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