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- PDB-3wjj: Crystal structure of IIb selective Fc variant, Fc(P238D), in comp... -

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Basic information

Entry
Database: PDB / ID: 3wjj
TitleCrystal structure of IIb selective Fc variant, Fc(P238D), in complex with FcgRIIb
Components
  • Ig gamma-1 chain C region
  • Low affinity immunoglobulin gamma Fc region receptor II-b
KeywordsIMMUNE SYSTEM / RECEPTOR COMPLEX / FC RECEPTOR / ANTIBODY
Function / homology
Function and homology information


negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of acute inflammatory response to antigenic stimulus ...negative regulation of type I hypersensitivity / negative regulation of antibody-dependent cellular cytotoxicity / immune effector process / follicular dendritic cell activation / immune complex clearance by monocytes and macrophages / regulation of B cell antigen processing and presentation / regulation of immune complex clearance by monocytes and macrophages / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / negative regulation of acute inflammatory response to antigenic stimulus / positive regulation of humoral immune response / negative regulation of dendritic cell antigen processing and presentation / negative regulation of humoral immune response mediated by circulating immunoglobulin / low-affinity IgG receptor activity / negative regulation of immunoglobulin production / negative regulation of cytotoxic T cell degranulation / negative regulation of B cell activation / follicular B cell differentiation / negative regulation of dendritic cell differentiation / negative regulation of B cell receptor signaling pathway / regulation of dendritic spine maintenance / negative regulation of macrophage activation / IgG receptor activity / mature B cell differentiation involved in immune response / regulation of adaptive immune response / cellular response to molecule of bacterial origin / negative regulation of immune response / Fc-gamma receptor signaling pathway / negative regulation of neutrophil activation / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / regulation of signaling receptor activity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / immunoglobulin receptor binding / negative regulation of cytokine production / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / negative regulation of phagocytosis / phagocytosis, engulfment / Initial triggering of complement / negative regulation of interleukin-10 production / regulation of innate immune response / negative regulation of B cell proliferation / immunoglobulin mediated immune response / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / phagocytosis / antigen binding / positive regulation of phagocytosis / cerebellum development / receptor-mediated endocytosis / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / response to bacterium / positive regulation of JNK cascade / defense response / antigen processing and presentation of exogenous peptide antigen via MHC class II / Regulation of actin dynamics for phagocytic cup formation / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / antibacterial humoral response / amyloid-beta binding / cell body / Interleukin-4 and Interleukin-13 signaling / blood microparticle / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / external side of plasma membrane / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Low affinity immunoglobulin gamma Fc region receptor II-b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKadono, S. / Mimoto, F. / Katada, H. / Igawa, T. / Kuramochi, T. / Muraoka, M. / Wada, Y. / Haraya, K. / Miyazaki, T. / Hattori, K.
CitationJournal: Protein Eng.Des.Sel. / Year: 2013
Title: Engineered antibody Fc variant with selectively enhanced Fc gamma RIIb binding over both Fc gamma RIIaR131 and Fc gamma RIIaH131.
Authors: Mimoto, F. / Katada, H. / Kadono, S. / Igawa, T. / Kuramochi, T. / Muraoka, M. / Wada, Y. / Haraya, K. / Miyazaki, T. / Hattori, K.
History
DepositionOct 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Other
Revision 1.2Jun 20, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
C: Low affinity immunoglobulin gamma Fc region receptor II-b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3935
Polymers72,1423
Non-polymers3,2512
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.850, 76.010, 115.080
Angle α, β, γ (deg.)90.000, 100.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 25942.264 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 99-328 / Mutation: P238D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Protein Low affinity immunoglobulin gamma Fc region receptor II-b / IgG Fc receptor II-b / CDw32 / Fc-gamma RII-b / Fc-gamma-RIIb / FcRII-b


Mass: 20257.516 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 45-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD32, FCG2, FCGR2B, FCGR2C, IGFR2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P31994
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG 3350, 0.1M Bis-Tris, 0.2M ammonium acetate, 2.7% D-galactose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→41.5 Å / Num. all: 25593 / Num. obs: 25455 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 53.69 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1840 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.2157 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8049 / SU B: 10.617 / SU ML: 0.234 / SU R Cruickshank DPI: 0.6047 / SU Rfree: 0.3217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.605 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 1294 5.1 %RANDOM
Rwork0.2301 ---
all0.2323 24270 --
obs0.2323 24146 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 127.36 Å2 / Biso mean: 63.4889 Å2 / Biso min: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å20 Å2-0.11 Å2
2---1.44 Å2-0 Å2
3---4.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 220 130 4810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194826
X-RAY DIFFRACTIONr_angle_refined_deg0.982.0036640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06924.974189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6511512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213557
X-RAY DIFFRACTIONr_mcbond_it1.646.4312325
X-RAY DIFFRACTIONr_mcangle_it2.9139.6392901
X-RAY DIFFRACTIONr_scbond_it1.4486.3472501
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 94 -
Rwork0.286 1728 -
all-1822 -
obs-1822 98.38 %

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