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- PDB-5mn2: Cocrystal structure of Fc gamma receptor IIIa interacting with Af... -

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Basic information

Entry
Database: PDB / ID: 5mn2
TitleCocrystal structure of Fc gamma receptor IIIa interacting with Affimer G3, a specific binding protein which blocks IgG binding to the receptor.
Components
  • Affimer G3
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / Fc gamma receptor IIIa Affimer Allosteric 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
: / Nuclear Transport Factor 2; Chain: A, - #10 / Immunoglobulin domain / Nuclear Transport Factor 2; Chain: A, / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...: / Nuclear Transport Factor 2; Chain: A, - #10 / Immunoglobulin domain / Nuclear Transport Factor 2; Chain: A, / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha 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. / Owen, R.L. / Tomlinson, D.C. / Baxter, E.W. / Nettleship, J.E. / Waterhouse, M.P. / Harris, S.A. / Owens, R.J. / McPherson, M.J. / Morgan, A.W. ...Robinson, J.I. / Owen, R.L. / Tomlinson, D.C. / Baxter, E.W. / Nettleship, J.E. / Waterhouse, M.P. / Harris, S.A. / Owens, R.J. / McPherson, M.J. / Morgan, A.W. / Tiede, C. / Goldman, A. / Thomsen, M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Arthritis Research UK19764 United Kingdom
Ann Wolks Memorial Fund650810 United Kingdom
NIHR United Kingdom
Medical Research Council (United Kingdom)MR/K018779/1 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 12, 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 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 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 1.5May 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 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low affinity immunoglobulin gamma Fc region receptor III-A
B: Low affinity immunoglobulin gamma Fc region receptor III-A
C: Affimer G3
D: Affimer G3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,24215
Polymers63,1954
Non-polymers2,04711
Water2,630146
1
A: Low affinity immunoglobulin gamma Fc region receptor III-A
D: Affimer G3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,09610
Polymers31,5982
Non-polymers1,4988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Low affinity immunoglobulin gamma Fc region receptor III-A
C: Affimer G3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1465
Polymers31,5982
Non-polymers5493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.985, 59.925, 100.001
Angle α, β, γ (deg.)90.00, 102.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#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: 20076.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mRNA / Source: (gene. exp.) Homo sapiens (human) / Tissue: Whole blood / Gene: FCGR3A, CD16A, FCG3, FCGR3, IGFR3 / Variant: 158F / Plasmid: pOPING / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P08637
#2: Protein Affimer G3


Mass: 11521.153 Da / Num. of mol.: 2
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, 7 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.: 7
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, 150 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20.0% v/v Glycerol 16.0% w/v Polyethylene glycol 8000 0.04 M Potassium di-Hydrogen Phosphate

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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 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.35→51.1 Å / Num. obs: 30227 / % possible obs: 95.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.049 / Net I/σ(I): 15.7
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata processing
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→43.39 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 1510 5 %
Rwork0.2055 --
obs0.2075 30208 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 127 146 4289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024311
X-RAY DIFFRACTIONf_angle_d0.4595883
X-RAY DIFFRACTIONf_dihedral_angle_d12.8072505
X-RAY DIFFRACTIONf_chiral_restr0.041669
X-RAY DIFFRACTIONf_plane_restr0.003739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.42590.37061650.28572620X-RAY DIFFRACTION97
2.4259-2.51260.3371320.28272671X-RAY DIFFRACTION97
2.5126-2.61320.3661460.27842605X-RAY DIFFRACTION97
2.6132-2.73210.29971340.26192622X-RAY DIFFRACTION97
2.7321-2.87610.27991230.23712626X-RAY DIFFRACTION97
2.8761-3.05630.28191370.23862625X-RAY DIFFRACTION96
3.0563-3.29220.28081090.23382640X-RAY DIFFRACTION96
3.2922-3.62330.271400.20832597X-RAY DIFFRACTION95
3.6233-4.14730.23261520.18292550X-RAY DIFFRACTION94
4.1473-5.22370.17211310.16282567X-RAY DIFFRACTION93
5.2237-43.39730.22481410.19882575X-RAY DIFFRACTION91

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