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Basic information

Entry
Database: PDB / ID: 5vu0
TitleCrystal structure of the complex between afucosylated/galactosylated human IgG1 Fc and Fc gamma receptor IIIa (CD16A) with Man5 N-glycans
Components
  • Immunoglobulin gamma-1 heavy chain
  • Low affinity immunoglobulin gamma Fc region receptor III-A
KeywordsIMMUNE SYSTEM / Complex / glycosylated
Function / homology
Function and homology information


immune receptor activity / low-affinity IgG receptor activity / IgG receptor activity / natural killer cell degranulation / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell mediated cytotoxicity / natural killer cell activation / antibody-dependent cellular cytotoxicity ...immune receptor activity / low-affinity IgG receptor activity / IgG receptor activity / natural killer cell degranulation / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / macrophage activation / natural killer cell mediated cytotoxicity / natural killer cell activation / antibody-dependent cellular cytotoxicity / IgG binding / positive regulation of natural killer cell proliferation / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / antigen binding / calcium-mediated signaling / FCGR3A-mediated phagocytosis / 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 / antibacterial humoral response / blood microparticle / membrane => GO:0016020 / cell surface receptor signaling pathway / immune response / external side of plasma membrane / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
DI(HYDROXYETHYL)ETHER / Low affinity immunoglobulin gamma Fc region receptor III-A / Low affinity immunoglobulin gamma Fc region receptor III-A / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsSubedi, G.S. / Marcella, A.M. / Barb, A.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115489 United States
Argonne National LaboratoryGUP-48455 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Antibody Fucosylation Lowers the Fc gamma RIIIa/CD16a Affinity by Limiting the Conformations Sampled by the N162-Glycan.
Authors: Falconer, D.J. / Subedi, G.P. / Marcella, A.M. / Barb, A.W.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
C: Low affinity immunoglobulin gamma Fc region receptor III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,09525
Polymers68,7533
Non-polymers4,34322
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Human Fc dimer and one Fc gamma receptor IIIa molecule.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.069, 48.846, 134.927
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1131-

HOH

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Components

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Antibody / Protein , 2 types, 3 molecules ABC

#1: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 24512.725 Da / Num. of mol.: 2 / Fragment: Fc region (UNP residues 230-446)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Protein Low affinity immunoglobulin gamma Fc region receptor III-A


Mass: 19727.068 Da / Num. of mol.: 1 / Mutation: N38Q, N74Q, F158V, N169Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR3A / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: H0Y755, UniProt: P08637*PLUS

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Sugars , 2 types, 4 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1479.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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][a2112h-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#7: 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.: 2
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, 272 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris Propane pH 7.5, 16% PEG 20k, 100 mM Potassium thiocyanate, Cryo protection - 20% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→131.05 Å / Num. obs: 36958 / % possible obs: 98.52 % / Redundancy: 4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.39
Reflection shellResolution: 2.26→2.336 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.6841 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3723 / % possible all: 96.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6X

1l6x


Resolution: 2.26→10 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.415 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23731 1975 5.4 %RANDOM
Rwork0.19167 ---
obs0.19418 34512 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.184 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å2-0 Å20.94 Å2
2---0.61 Å2-0 Å2
3---2.71 Å2
Refinement stepCycle: 1 / Resolution: 2.26→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 281 254 5267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195185
X-RAY DIFFRACTIONr_bond_other_d0.0030.024753
X-RAY DIFFRACTIONr_angle_refined_deg2.0372.0067075
X-RAY DIFFRACTIONr_angle_other_deg1.078311067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71124.747217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3651517
X-RAY DIFFRACTIONr_chiral_restr0.1080.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021104
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8822.7722387
X-RAY DIFFRACTIONr_mcbond_other1.882.7712386
X-RAY DIFFRACTIONr_mcangle_it3.1484.1312977
X-RAY DIFFRACTIONr_mcangle_other3.1484.1322978
X-RAY DIFFRACTIONr_scbond_it2.1333.0812797
X-RAY DIFFRACTIONr_scbond_other2.1313.0812797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5114.5324095
X-RAY DIFFRACTIONr_long_range_B_refined5.88621.7825383
X-RAY DIFFRACTIONr_long_range_B_other5.88421.7825383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.256→2.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 138 -
Rwork0.28 2403 -
obs--96.54 %
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)
11.110.09920.19690.82090.32730.31170.0044-0.0506-0.1622-0.064-0.0342-0.0133-0.03170.02340.02970.15070.0185-0.01940.08240.01940.0644124.72812.7613.326
21.801-0.29380.36990.67680.62860.8606-0.1238-0.3461-0.2918-0.04910.03980.1889-0.1218-0.03260.08390.1169-0.01050.00320.18380.04160.0927109.03131.50626.631
30.8366-0.38290.22641.8570.53120.6534-0.1273-0.52940.0393-0.11730.0267-0.3693-0.1148-0.24740.10070.16170.0797-0.03220.45720.01790.2394150.68440.74245.285
40.3325-0.06670.03370.21870.0820.0463-0.0154-0.1342-0.0613-0.01280.00540.0451-0.01810.00410.00990.2033-0.0004-0.0410.23280.02260.025125.41724.28823.671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A234 - 443
2X-RAY DIFFRACTION1A1001 - 1008
3X-RAY DIFFRACTION2B232 - 444
4X-RAY DIFFRACTION2B1001 - 1008
5X-RAY DIFFRACTION3C3 - 174
6X-RAY DIFFRACTION3C201 - 202
7X-RAY DIFFRACTION4A1101 - 1213
8X-RAY DIFFRACTION4B1101 - 1188
9X-RAY DIFFRACTION4C301 - 353

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