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- PDB-6mj3: CRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 Fc Frag... -

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Basic information

Entry
Database: PDB / ID: 6mj3
TitleCRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 Fc Fragment-Fc-GAMMA RECEPTOR III complex
Components
  • Igg1 Fc
  • Low affinity immunoglobulin gamma Fc region receptor III
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / FC GAMMA RECEPTOR III
Function / homology
Function and homology information


natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor signaling pathway / natural killer cell mediated cytotoxicity / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction ...natural killer cell degranulation / IgG receptor activity / Fc-gamma receptor signaling pathway / natural killer cell mediated cytotoxicity / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / complement activation, classical pathway / calcium-mediated signaling / antigen binding / antibacterial humoral response / cell surface receptor signaling pathway / blood microparticle / external side of plasma membrane / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsGohain, N. / 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)R01AI16274 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 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _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.auth_asym_id / _atom_site.auth_seq_id ..._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_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
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

Downloads & links

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Assembly

Deposited unit
A: Igg1 Fc
B: Igg1 Fc
D: Igg1 Fc
E: Igg1 Fc
C: Low affinity immunoglobulin gamma Fc region receptor III
F: Low affinity immunoglobulin gamma Fc region receptor III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,06813
Polymers144,5516
Non-polymers6,5177
Water00
1
A: Igg1 Fc
B: Igg1 Fc
C: Low affinity immunoglobulin gamma Fc region receptor III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6457
Polymers72,2763
Non-polymers3,3694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Igg1 Fc
E: Igg1 Fc
F: Low affinity immunoglobulin gamma Fc region receptor III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4236
Polymers72,2763
Non-polymers3,1483
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.108, 71.270, 135.521
Angle α, β, γ (deg.)90.00, 119.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Igg1 Fc


Mass: 25143.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human) / References: UniProt: F6RL33
#2: Protein Low affinity immunoglobulin gamma Fc region receptor III / IgG Fc receptor III / Fc-gamma RIII / FcRIII


Mass: 21988.773 Da / Num. of mol.: 2 / 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
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 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]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 4000, 0.1M HEPES pH 7.0, 0.1M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.8→66.51 Å / Num. obs: 14678 / % possible obs: 83.9 % / Redundancy: 2.3 % / CC1/2: 0.96 / Rpim(I) all: 0.145 / Rsym value: 0.184 / Net I/σ(I): 3.4
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2222 / CC1/2: 0.75 / Rpim(I) all: 0.496 / Rsym value: 0.638 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E4K

1e4k


Resolution: 3.8→66.51 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 33.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3236 1196 4.65 %
Rwork0.2761 --
obs0.2782 25699 75.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→66.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9418 0 438 0 9856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610159
X-RAY DIFFRACTIONf_angle_d1.14813906
X-RAY DIFFRACTIONf_dihedral_angle_d9.3036084
X-RAY DIFFRACTIONf_chiral_restr0.0671633
X-RAY DIFFRACTIONf_plane_restr0.0071710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.95220.39791470.35492756X-RAY DIFFRACTION77
3.9522-4.1320.3531210.33622728X-RAY DIFFRACTION75
4.132-4.34980.38211600.3012677X-RAY DIFFRACTION75
4.3498-4.62230.31291140.27882485X-RAY DIFFRACTION68
4.6223-4.9790.29911440.26452874X-RAY DIFFRACTION80
4.979-5.47990.31611380.25232823X-RAY DIFFRACTION78
5.4799-6.27230.33961400.26992711X-RAY DIFFRACTION75
6.2723-7.90040.30871080.27962618X-RAY DIFFRACTION72
7.9004-66.51970.26891240.23552831X-RAY DIFFRACTION78
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)
12.88521.9923-1.55222.5938-0.96172.77590.3234-0.03780.40420.6455-0.19610.2459-0.5447-0.309-0.07320.53520.0581-0.03250.5518-0.15940.6453-40.10642.299743.0075
21.87821.3630.80983.53171.61652.43490.19360.2055-0.4547-0.0999-0.208-0.2213-0.01390.07450.01620.36740.10160.01690.86660.00020.5752-25.964727.163522.507
32.24511.14930.03722.9554-1.09351.203-0.08390.4730.091-0.16530.28540.38970.0486-0.0487-0.23680.5348-0.007-0.02980.8055-0.05130.6384-104.871462.197222.1685
42.82011.74661.39721.75891.60822.87350.32520.1705-0.19780.50260.0526-0.60620.72820.3789-0.36820.76530.1782-0.08830.6207-0.05381.0009-90.276642.662637.7158
52.5252-0.41460.99761.73830.82795.2617-0.1663-0.238-0.0681-0.0849-0.02040.454-0.2477-0.66090.24590.5568-0.11970.06311.0077-0.10040.5834-71.547415.08510.9577
63.50480.57491.18252.71260.03044.4804-0.18460.06080.31520.26310.5601-0.2704-0.2371-0.0755-0.38410.6373-0.05880.15630.7159-0.20210.742-67.983283.451353.6675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 237 through 443)
2X-RAY DIFFRACTION2(chain 'B' and resid 234 through 443)
3X-RAY DIFFRACTION3(chain 'D' and resid 237 through 444)
4X-RAY DIFFRACTION4(chain 'E' and resid 234 through 444)
5X-RAY DIFFRACTION5(chain 'C' and resid 3 through 171)
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 171)

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