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- PDB-9pru: Complex of the 3G8 Fab bound to Fc gamma receptor 3a / CD16a F158... -

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Basic information

Entry
Database: PDB / ID: 9pru
TitleComplex of the 3G8 Fab bound to Fc gamma receptor 3a / CD16a F158 allotype
Components
  • 3G8 Fab Heavy Chain
  • 3G8 Fab light chain
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / antigen-binding Fragment Fc gamma receptor N-glycan glycoprotein
Function / homology
Function and homology information


immune receptor activity / low-affinity IgG receptor activity / natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding ...immune receptor activity / low-affinity IgG receptor activity / natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / FCGR activation / Role of phospholipids in phagocytosis / FCGR3A-mediated IL10 synthesis / FCGR3A-mediated phagocytosis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / calcium-mediated signaling / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / immune response / external side of plasma membrane / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / 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 III-A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBarb, A.W. / Lanzilotta, W.N. / Kremer, P.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI148114 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI187028 United States
CitationJournal: Structure / Year: 2025
Title: The impact of N-glycan conformational entropy on the binding affinity of Fc gamma receptor IIIa/CD16a.
Authors: Kremer, P.G. / Tolbert, W.D. / Gazaway, E. / Hernandez, B.G. / Korzeniowski, M.K. / Dyba, Z.A. / Grelsson, T. / Grant, O.C. / Lanzilotta, W.N. / Pazgier, M. / Woods, R.J. / Barb, A.W.
History
DepositionJul 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3G8 Fab light chain
B: 3G8 Fab Heavy Chain
C: 3G8 Fab light chain
D: 3G8 Fab Heavy Chain
E: 3G8 Fab light chain
F: 3G8 Fab Heavy Chain
G: 3G8 Fab light chain
H: 3G8 Fab Heavy Chain
W: Low affinity immunoglobulin gamma Fc region receptor III-A
X: Low affinity immunoglobulin gamma Fc region receptor III-A
Y: Low affinity immunoglobulin gamma Fc region receptor III-A
Z: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,44727
Polymers270,99812
Non-polymers3,45015
Water22,4291245
1
A: 3G8 Fab light chain
B: 3G8 Fab Heavy Chain
W: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6496
Polymers67,7493
Non-polymers9003
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-20 kcal/mol
Surface area26890 Å2
MethodPISA
2
C: 3G8 Fab light chain
D: 3G8 Fab Heavy Chain
X: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6496
Polymers67,7493
Non-polymers9003
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-25 kcal/mol
Surface area26570 Å2
MethodPISA
3
E: 3G8 Fab light chain
F: 3G8 Fab Heavy Chain
Y: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5107
Polymers67,7493
Non-polymers7614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-22 kcal/mol
Surface area26220 Å2
MethodPISA
4
G: 3G8 Fab light chain
H: 3G8 Fab Heavy Chain
Z: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6398
Polymers67,7493
Non-polymers8895
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-53 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.062, 130.594, 170.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules WXYZ

#3: Protein
Low affinity immunoglobulin gamma Fc region receptor III-A / IgG Fc receptor III-A / CD16-II / CD16a antigen / Fc-gamma RIII-alpha / Fc-gamma RIII / Fc-gamma ...IgG Fc receptor III-A / CD16-II / CD16a antigen / Fc-gamma RIII-alpha / Fc-gamma RIII / Fc-gamma RIIIa / FcRIII / FcRIIIa / FcgammaRIIIA / FcR-10 / IgG Fc receptor III-2


Mass: 20118.471 Da / Num. of mol.: 4 / Mutation: N38Q N74Q N169Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR3A, CD16A, FCG3, FCGR3, IGFR3 / Production host: Homo sapiens (human) / References: UniProt: P08637

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
3G8 Fab light chain


Mass: 23953.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
3G8 Fab Heavy Chain


Mass: 23677.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Sugars , 3 types, 8 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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: obtained synthetically
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
#9: 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 4 types, 1252 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1245 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.82
Details: 0.2 M KCl, 0.1 M Bis-Tris, 20% PEG3350, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 230340 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.94 / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.8
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 1 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.28 --
Rwork0.23 --
obs0.23 230340 100 %
Refinement stepCycle: LAST / Resolution: 1.9→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18016 0 223 1245 19484
LS refinement shellHighest resolution: 1.9 Å
RfactorNum. reflection% reflection
Rfree0.3824 --
Rwork0.3495 --
all-9767 -
obs--99.9 %

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