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- PDB-7kcz: CRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 FC FRAG... -

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Basic information

Entry
Database: PDB / ID: 7kcz
TitleCRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 FC FRAGMENT- FC-GAMMA RECEPTOR III COMPLEX V158 MUTANT
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 / Immunoglobulin-like fold
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: 3.15 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 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
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Oct 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
C: Low affinity immunoglobulin gamma Fc region receptor III
D: IgG1 Fc
E: IgG1 Fc
F: Low affinity immunoglobulin gamma Fc region receptor III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,74316
Polymers144,5236
Non-polymers8,22010
Water1448
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)76,3798
Polymers72,2613
Non-polymers4,1185
Water543
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)76,3638
Polymers72,2613
Non-polymers4,1025
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.690, 70.110, 135.410
Angle α, β, γ (deg.)90.00, 119.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody / Protein / Non-polymers , 3 types, 14 molecules ABDECF

#1: Antibody
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 line (production host): HEK293 / 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: 21974.746 Da / Num. of mol.: 2 / Mutation: I158V, N38Q, N169Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: FCGR3 / Cell line (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A3RFZ7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 10 molecules

#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: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 4
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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Details

Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 0.2 M lithium sulfate, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.15→60.11 Å / Num. obs: 92773 / % possible obs: 96.4 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rpim(I) all: 0.101 / Rsym value: 0.15 / Net I/σ(I): 3
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 3.1 % / Num. unique obs: 4297 / CC1/2: 0.701 / Rpim(I) all: 0.605 / Rsym value: 0.91 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MJ3

6mj3


Resolution: 3.15→60.11 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 35.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3032 2715 4.87 %
Rwork0.2694 --
obs0.271 55714 93.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→60.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9451 0 551 8 10010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110279
X-RAY DIFFRACTIONf_angle_d1.54814008
X-RAY DIFFRACTIONf_dihedral_angle_d17.6881612
X-RAY DIFFRACTIONf_chiral_restr0.0851685
X-RAY DIFFRACTIONf_plane_restr0.011720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.210.40391340.39962775X-RAY DIFFRACTION93
3.21-3.270.31511570.37062736X-RAY DIFFRACTION93
3.27-3.340.36341280.34952834X-RAY DIFFRACTION93
3.34-3.410.41071220.34312573X-RAY DIFFRACTION88
3.41-3.490.39211580.35032511X-RAY DIFFRACTION84
3.49-3.570.38461560.33012838X-RAY DIFFRACTION96
3.57-3.670.34571840.33122889X-RAY DIFFRACTION97
3.67-3.780.40211550.30632844X-RAY DIFFRACTION97
3.78-3.90.35141540.30722880X-RAY DIFFRACTION96
3.9-4.040.32941310.27912846X-RAY DIFFRACTION95
4.04-4.20.29141380.26182831X-RAY DIFFRACTION95
4.2-4.390.3241520.24292755X-RAY DIFFRACTION93
4.39-4.630.23181240.21932563X-RAY DIFFRACTION86
4.63-4.910.26051390.2152906X-RAY DIFFRACTION97
4.92-5.290.2161490.20622845X-RAY DIFFRACTION97
5.29-5.830.2611360.23282936X-RAY DIFFRACTION97
5.83-6.670.29571410.26632688X-RAY DIFFRACTION90
6.67-8.40.27761190.25712876X-RAY DIFFRACTION96
8.4-60.110.25251380.24232873X-RAY DIFFRACTION96
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)
12.71041.4044-0.28441.6006-0.36231.8830.2103-0.23580.31320.2385-0.16520.1943-0.5867-0.45950.00580.52280.1211-0.14470.9557-0.10990.3276-40.430342.041442.8149
23.09132.0180.61243.56131.40431.84730.10120.2256-0.44910.2628-0.0578-0.42850.12720.173-0.10370.2231-0.0266-0.15471.10130.09320.2946-26.371526.808722.6776
31.15920.50691.44461.03261.38942.8271-0.1925-0.04070.178-0.2139-0.19570.107-0.329-0.28660.27790.29-0.0942-0.37332.0404-0.1620.0352-72.319115.373711.4247
41.74741.1873-0.44022.5162-1.09191.01090.09460.3638-0.14180.02560.2020.20670.10050.0552-0.23520.27-0.0068-0.06441.2412-0.11020.417-105.884961.279222.5
54.75591.60180.59921.96640.34551.56460.16290.4599-0.9357-0.03440.1944-0.3620.50250.5767-0.26450.4810.2108-0.20330.9757-0.17480.6371-91.489541.95338.141
62.14960.29291.4411.83640.0823.2411-0.1982-0.23250.03440.21950.2977-0.1688-0.267-0.4089-0.04270.47140.0304-0.02471.453-0.31280.4531-68.615382.473153.4732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 235 through 443)
2X-RAY DIFFRACTION2(chain 'B' and resid 232 through 443)
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 171)
4X-RAY DIFFRACTION4(chain 'D' and resid 235 through 443)
5X-RAY DIFFRACTION5(chain 'E' and resid 232 through 443)
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 171)

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