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- PDB-5occ: Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5occ
TitleCrystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (6G08)
Components
  • 6G08 Fab Light Chain
  • 6G08 Fab heavy chain
  • Low affinity immunoglobulin gamma Fc region receptor II-b
KeywordsIMMUNE SYSTEM / cd32b / Complex / Fab / mAb
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 neutrophil activation / negative regulation of dendritic cell antigen processing and presentation / negative regulation of B cell receptor signaling pathway / negative regulation of humoral immune response mediated by circulating immunoglobulin / low-affinity IgG receptor activity / follicular B cell differentiation / negative regulation of cytotoxic T cell degranulation / negative regulation of immunoglobulin production / cellular response to molecule of bacterial origin / negative regulation of dendritic cell differentiation / regulation of dendritic spine maintenance / negative regulation of B cell activation / IgG receptor activity / regulation of adaptive immune response / mature B cell differentiation involved in immune response / negative regulation of macrophage activation / Fc-gamma receptor signaling pathway / negative regulation of immune response / regulation of signaling receptor activity / negative regulation of phagocytosis / IgG binding / antibody-dependent cellular cytotoxicity / negative regulation of cytokine production / phagocytosis, engulfment / negative regulation of interleukin-10 production / regulation of innate immune response / negative regulation of B cell proliferation / immunoglobulin mediated immune response / phagocytosis / positive regulation of phagocytosis / cerebellum development / receptor-mediated endocytosis / positive regulation of JNK cascade / response to bacterium / defense response / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / amyloid-beta binding / cell body / dendritic spine / cell surface receptor signaling pathway / inflammatory response / external side of plasma membrane / protein-containing complex binding / plasma membrane
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 / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Low affinity immunoglobulin gamma Fc region receptor II-b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsTews, I. / Orr, C.
CitationJournal: Biophys. J. / Year: 2018
Title: Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering.
Authors: Sutton, E.J. / Bradshaw, R.T. / Orr, C.M. / Frendeus, B. / Larsson, G. / Teige, I. / Cragg, M.S. / Tews, I. / Essex, J.W.
History
DepositionJun 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low affinity immunoglobulin gamma Fc region receptor II-b
H: 6G08 Fab heavy chain
L: 6G08 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5518
Polymers65,6263
Non-polymers9255
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-26 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.230, 75.020, 134.950
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, 1 molecules A

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


Mass: 19713.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Crystal structure does not resolve residues 1-10, 32-36. Residue 44 modelled as ALA due to lack of density.
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2B, CD32, FCG2, IGFR2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): EBNA / References: UniProt: P31994

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Antibody , 2 types, 2 molecules HL

#2: Antibody 6G08 Fab heavy chain


Mass: 23091.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): EBNA
#3: Antibody 6G08 Fab Light Chain


Mass: 22820.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Terminal serine is not resolved in resolved in electron density
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): EBNA

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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)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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, 108 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MES, 0.01M Zinc Chloride, 20% PEG 6000, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→134.95 Å / Num. obs: 23884 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.5→134.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 24.589 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26077 1281 5.1 %RANDOM
Rwork0.19229 ---
obs0.19585 23884 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.578 Å2
Baniso -1Baniso -2Baniso -3
1--3.81 Å20 Å20 Å2
2--3.17 Å20 Å2
3---0.64 Å2
Refinement stepCycle: 1 / Resolution: 2.5→134.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4513 0 59 105 4677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194689
X-RAY DIFFRACTIONr_bond_other_d0.0020.024135
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.966396
X-RAY DIFFRACTIONr_angle_other_deg1.15439686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3375596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29324.804179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.70415713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5581514
X-RAY DIFFRACTIONr_chiral_restr0.1190.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215191
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02892
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3432.2372396
X-RAY DIFFRACTIONr_mcbond_other1.3312.2352395
X-RAY DIFFRACTIONr_mcangle_it2.2863.3482988
X-RAY DIFFRACTIONr_mcangle_other2.2863.352989
X-RAY DIFFRACTIONr_scbond_it1.7772.3612293
X-RAY DIFFRACTIONr_scbond_other1.7772.3612293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5553.473409
X-RAY DIFFRACTIONr_long_range_B_refined5.24726.0174911
X-RAY DIFFRACTIONr_long_range_B_other5.24825.9694906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 99 -
Rwork0.331 1707 -
obs--98.9 %
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)
13.3595-1.3693-0.42191.635-0.44392.6726-0.03340.1875-0.1403-0.29040.1653-0.54190.24840.5999-0.13180.33730.00520.14620.6079-0.14490.543914.542624.9952-55.46
20.69470.173-0.6391.095-1.44143.9315-0.08680.03910.073-0.1277-0.08890.09590.12390.07570.17570.03450.0382-0.02840.1401-0.00960.1260.351622.4698-17.9496
30.60310.2525-1.23010.4037-0.74784.8996-0.01320.10250.2062-0.05930.06850.1190.1401-0.437-0.05530.01450.0060.00220.20020.00410.1441-16.460928.3334-16.4602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 303
2X-RAY DIFFRACTION2H1 - 222
3X-RAY DIFFRACTION3L1 - 216

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