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- PDB-5ml9: Cocrystal structure of Fc gamma receptor IIIa interacting with Af... -

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Basic information

Entry
Database: PDB / ID: 5ml9
TitleCocrystal structure of Fc gamma receptor IIIa interacting with Affimer F4, a specific binding protein which blocks IgG binding to the receptor.
Components
  • Affimer F4 with specificity for Fc gamma receptor IIIa
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / Fc gamma receptor IIIa Affimer Competitive inhibitor FCGR3A
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 / positive regulation of natural killer cell proliferation / antibody-dependent cellular cytotoxicity ...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 / positive regulation of natural killer cell proliferation / antibody-dependent cellular cytotoxicity / IgG binding / natural killer cell mediated cytotoxicity / FCGR activation / Role of phospholipids in phagocytosis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / FCGR3A-mediated IL10 synthesis / FCGR3A-mediated phagocytosis / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...: / Immunoglobulin domain / 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
DI(HYDROXYETHYL)ETHER / Low affinity immunoglobulin gamma Fc region receptor III-A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRobinson, J.I. / Tomlinson, D.C. / Baxter, E.W. / Owen, R.L. / Thomsen, M. / Win, S.J. / Nettleship, J.E. / Tiede, C. / Foster, R.J. / Waterhouse, M.P. ...Robinson, J.I. / Tomlinson, D.C. / Baxter, E.W. / Owen, R.L. / Thomsen, M. / Win, S.J. / Nettleship, J.E. / Tiede, C. / Foster, R.J. / Waterhouse, M.P. / Harris, S.A. / Owens, R.J. / Fishwick, C.W.G. / Goldman, A. / McPherson, M.J. / Morgan, A.W.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Arthritis Research UK19764 United Kingdom
Ann Wilks Memorial Fund650810 United Kingdom
NIHRLMBRU United Kingdom
Medical Research Council (United Kingdom)MR/K018779/1 United Kingdom
European Union708051 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Affimer proteins inhibit immune complex binding to Fc gamma RIIIa with high specificity through competitive and allosteric modes of action.
Authors: Robinson, J.I. / Baxter, E.W. / Owen, R.L. / Thomsen, M. / Tomlinson, D.C. / Waterhouse, M.P. / Win, S.J. / Nettleship, J.E. / Tiede, C. / Foster, R.J. / Owens, R.J. / Fishwick, C.W.G. / ...Authors: Robinson, J.I. / Baxter, E.W. / Owen, R.L. / Thomsen, M. / Tomlinson, D.C. / Waterhouse, M.P. / Win, S.J. / Nettleship, J.E. / Tiede, C. / Foster, R.J. / Owens, R.J. / Fishwick, C.W.G. / Harris, S.A. / Goldman, A. / McPherson, M.J. / Morgan, A.W.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 III-A
B: Affimer F4 with specificity for Fc gamma receptor IIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,67713
Polymers33,2652
Non-polymers1,41211
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-38 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.481, 72.587, 96.451
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 , 2 types, 2 molecules AB

#1: Protein Low affinity immunoglobulin gamma Fc region receptor III-A / CD16a antigen / Fc-gamma RIII-alpha / FcRIIIa / FcR-10 / IgG Fc receptor III-2


Mass: 20028.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Whole blood / Gene: FCGR3A, CD16A, FCG3, FCGR3, IGFR3 / Variant: 158V / Plasmid: pOPING / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P08637
#2: Protein Affimer F4 with specificity for Fc gamma receptor IIIa


Mass: 13236.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Sugars , 1 types, 3 molecules

#3: 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.: 3
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 , 4 types, 92 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium Sulphate 0.1 M Sodium Cacodylate pH=6.50 0.2 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.34→56.5 Å / Num. obs: 16390 / % possible obs: 95.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 7.1
Reflection shellResolution: 2.34→2.43 Å / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A SUBSECTION OF A COMPLEX OF AN ADHIRON BOUND TO A SOLUBLE PROTEIN (MANUSCRIPT IN PREPARATION) WAS USED AS A SEARCH MODEL.

Resolution: 2.35→48.74 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 832 5.15 %
Rwork0.219 --
obs0.222 16155 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 75 84 2338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022310
X-RAY DIFFRACTIONf_angle_d0.4743143
X-RAY DIFFRACTIONf_dihedral_angle_d12.6361345
X-RAY DIFFRACTIONf_chiral_restr0.043346
X-RAY DIFFRACTIONf_plane_restr0.002395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.49730.33131310.32142493X-RAY DIFFRACTION95
2.4973-2.69010.38871460.29632601X-RAY DIFFRACTION97
2.6901-2.96080.32071190.26532565X-RAY DIFFRACTION96
2.9608-3.38920.2861590.23312573X-RAY DIFFRACTION97
3.3892-4.26960.24061380.1842558X-RAY DIFFRACTION94
4.2696-48.74960.22481390.18092533X-RAY DIFFRACTION89

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