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- PDB-6yax: Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6yax
TitleCrystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)
Components
  • 5C05 F(ab) heavy chain
  • 5C05 F(ab) light chain
  • Low affinity immunoglobulin gamma Fc region receptor II-c
KeywordsIMMUNE SYSTEM / CD32 CD32b Fc gamma receptor Fc gamma receptor II b Fab Complex
Function / homology
Function and homology information


IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / positive regulation of phagocytosis / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cell surface receptor signaling pathway / immune response / external side of plasma membrane / membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 II-c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFisher, H. / Tews, I. / Orr, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKS_3591 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)
Authors: Fisher, H. / Tews, I. / Orr, C.
History
DepositionMar 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: 5C05 F(ab) heavy chain
MMM: 5C05 F(ab) light chain
AAA: Low affinity immunoglobulin gamma Fc region receptor II-c
LLL: 5C05 F(ab) light chain
III: 5C05 F(ab) heavy chain
BBB: Low affinity immunoglobulin gamma Fc region receptor II-c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,41811
Polymers133,2926
Non-polymers1,1265
Water4,990277
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-35 kcal/mol
Surface area51360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.728, 95.728, 186.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 2 molecules AAABBB

#3: Protein Low affinity immunoglobulin gamma Fc region receptor II-c / IgG Fc receptor II-c / CDw32 / Fc-gamma RII-c / FcRII-c


Mass: 20455.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2C, CD32, FCG2, IGFR2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P31995

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Antibody , 2 types, 4 molecules HHHIIIMMMLLL

#1: Antibody 5C05 F(ab) heavy chain


Mass: 23210.949 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)
#2: Antibody 5C05 F(ab) light chain


Mass: 22979.346 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)

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Sugars , 2 types, 2 molecules

#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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 , 3 types, 280 molecules

#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2- propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1.0 M tris (base), BICINE, 40% v/v PEG 500 MME, 20% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→47.86 Å / Num. obs: 41024 / % possible obs: 99.3 % / Redundancy: 7.2 % / CC1/2: 0.995 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 3003 / CC1/2: 0.491

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCC

5occ


Resolution: 2.8→47.86 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: FREE R-VALUE / ESU R: 0.927 / ESU R Free: 0.355
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2644 1971 4.812 %
Rwork0.2299 --
all0.232 --
obs-40956 99.555 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.214 Å20 Å20 Å2
2--0.214 Å20 Å2
3----0.427 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8293 0 74 277 8644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138609
X-RAY DIFFRACTIONr_bond_other_d0.0360.0177564
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.6511734
X-RAY DIFFRACTIONr_angle_other_deg2.4271.57617664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55451083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87723.485373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.811151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861527
X-RAY DIFFRACTIONr_chiral_restr0.0490.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029583
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021715
X-RAY DIFFRACTIONr_nbd_refined0.1930.21376
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.27050
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23917
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.224
X-RAY DIFFRACTIONr_nbd_other0.230.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.25
X-RAY DIFFRACTIONr_mcbond_it3.0427.6754370
X-RAY DIFFRACTIONr_mcbond_other3.0427.6754369
X-RAY DIFFRACTIONr_mcangle_it4.76811.4825431
X-RAY DIFFRACTIONr_mcangle_other4.76811.4825432
X-RAY DIFFRACTIONr_scbond_it3.1877.8044239
X-RAY DIFFRACTIONr_scbond_other3.1877.8054240
X-RAY DIFFRACTIONr_scangle_it5.04111.6386300
X-RAY DIFFRACTIONr_scangle_other5.0411.6386301
X-RAY DIFFRACTIONr_lrange_it7.21586.788799
X-RAY DIFFRACTIONr_lrange_other7.21586.7788800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.8-2.8720.3671440.33428020.33630200.7280.72497.54970.328
2.872-2.950.3761470.3328090.33329570.7550.76799.96620.316
2.95-3.0360.3191470.30426990.30428500.7890.80699.85960.292
3.036-3.1290.321500.29326330.29427830.8260.8291000.273
3.129-3.2310.336940.2826160.28227100.8010.8421000.258
3.231-3.3440.2981140.26424920.26626060.8590.8741000.242
3.344-3.4690.2941400.25424020.25625430.870.88499.96070.232
3.469-3.610.3181180.25122840.25424030.8550.87999.95840.23
3.61-3.770.2951210.27422150.27523540.8770.8799.23530.245
3.77-3.9520.2741120.22521010.22822190.8970.91999.72960.209
3.952-4.1650.249980.220340.20221320.9230.9391000.187
4.165-4.4150.2291090.19118830.19319920.9210.9381000.181
4.415-4.7170.198820.17218130.17318970.9490.95899.89460.167
4.717-5.0910.201780.17316650.17517600.9530.95499.03410.172
5.091-5.5710.257890.19415030.19816400.9180.93597.07320.193
5.571-6.2180.249540.20814120.20914660.9170.9341000.203
6.218-7.1590.21590.21112450.21113040.9270.9331000.21
7.159-8.720.304480.20810680.21111160.8760.9231000.213
8.72-12.1320.184460.2018180.28640.9440.9531000.21
12.132-47.8640.25210.3134900.3115150.9110.89899.22330.384

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