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- PDB-6mjo: CRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) FC-GAMMA REC... -

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Basic information

Entry
Database: PDB / ID: 6mjo
TitleCRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) FC-GAMMA RECEPTOR III
ComponentsLow affinity immunoglobulin gamma Fc region receptor III
KeywordsIMMUNE SYSTEM / FC GAMMA RECEPTOR III
Function / homology
Function and homology information


IgG receptor activity / natural killer cell degranulation / Fc-gamma receptor signaling pathway / natural killer cell mediated cytotoxicity / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / calcium-mediated signaling / cell surface receptor signaling pathway ...IgG receptor activity / natural killer cell degranulation / Fc-gamma receptor signaling pathway / natural killer cell mediated cytotoxicity / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / calcium-mediated signaling / cell surface receptor signaling pathway / external side of plasma membrane / extracellular space / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor III-A
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVan, V. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: Front Immunol / Year: 2022
Title: Decoding human-macaque interspecies differences in Fc-effector functions: The structural basis for CD16-dependent effector function in Rhesus macaques.
Authors: Tolbert, W.D. / Gohain, N. / Kremer, P.G. / Hederman, A.P. / Nguyen, D.N. / Van, V. / Sherburn, R. / Lewis, G.K. / Finzi, A. / Pollara, J. / Ackerman, M.E. / Barb, A.W. / Pazgier, M.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Revision 2.1Oct 26, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Low affinity immunoglobulin gamma Fc region receptor III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4453
Polymers21,9891
Non-polymers1,4562
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.073, 63.960, 69.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Low affinity immunoglobulin gamma Fc region receptor III / IgG Fc receptor III / Fc-gamma RIII / FcRIII


Mass: 21988.773 Da / Num. of mol.: 1 / Mutation: N38Q, N169Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: FCGR3 / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human) / References: UniProt: A3RFZ7
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 25% PEG 3350 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2017
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 17804 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.067 / Net I/σ(I): 27.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 836 / CC1/2: 0.77 / Rpim(I) all: 0.435 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E4J

1e4j


Resolution: 1.9→33.989 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.83
RfactorNum. reflection% reflection
Rfree0.2178 814 4.58 %
Rwork0.182 --
obs0.1838 17763 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 97 87 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151558
X-RAY DIFFRACTIONf_angle_d1.6362133
X-RAY DIFFRACTIONf_dihedral_angle_d16.69934
X-RAY DIFFRACTIONf_chiral_restr0.091257
X-RAY DIFFRACTIONf_plane_restr0.007254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-2.01690.30271170.25142701X-RAY DIFFRACTION97
2.0169-2.17270.25531190.21862803X-RAY DIFFRACTION99
2.1727-2.39120.24681410.19912800X-RAY DIFFRACTION100
2.3912-2.73710.25931520.20962810X-RAY DIFFRACTION100
2.7371-3.4480.24631210.18942871X-RAY DIFFRACTION100
3.448-33.99470.18731640.1592964X-RAY DIFFRACTION100

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