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Basic information

Entry
Database: PDB / ID: 3sgj
TitleUnique carbohydrate-carbohydrate interactions are required for high affinity binding between FcgIII and antibodies lacking core fucose
Components
  • human Fc fragmentFragment crystallizable region
  • human Fcg3a receptor
KeywordsIMMUNE SYSTEM / receptor complex / Fc receptor / antibody
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 / complement-dependent 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 / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / positive regulation of natural killer cell proliferation / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / 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 / Regulation of Complement cascade / calcium-mediated signaling / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / 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 / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / cell surface receptor signaling pathway / immune response / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin 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 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
MALONATE ION / Immunoglobulin heavy constant gamma 1 / Low affinity immunoglobulin gamma Fc region receptor III-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFerrara, C. / Grau, S. / Jaeger, C. / Sondermann, P. / Bruenker, P. / Waldhauer, I. / Hennig, M. / Ruf, A. / Rufer, A.C. / Stihle, M. ...Ferrara, C. / Grau, S. / Jaeger, C. / Sondermann, P. / Bruenker, P. / Waldhauer, I. / Hennig, M. / Ruf, A. / Rufer, A.C. / Stihle, M. / Umana, P. / Benz, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Unique carbohydrate-carbohydrate interactions are required for high affinity binding between FcgammaRIII and antibodies lacking core fucose.
Authors: Ferrara, C. / Grau, S. / Jager, C. / Sondermann, P. / Brunker, P. / Waldhauer, I. / Hennig, M. / Ruf, A. / Rufer, A.C. / Stihle, M. / Umana, P. / Benz, J.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human Fc fragment
B: human Fc fragment
C: human Fcg3a receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4228
Polymers74,0583
Non-polymers4,3645
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint74 kcal/mol
Surface area31100 Å2
MethodPISA
2
C: human Fcg3a receptor
hetero molecules

A: human Fc fragment
B: human Fc fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4228
Polymers74,0583
Non-polymers4,3645
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint66 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.654, 88.478, 140.29
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein human Fc fragment / Fragment crystallizable region


Mass: 25336.688 Da / Num. of mol.: 2 / Fragment: unp residues 106-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: Protein human Fcg3a receptor


Mass: 23384.293 Da / Num. of mol.: 1 / Fragment: unp residues 19-208 / Mutation: N38Q, N74Q, N169Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD16A, FCG3, FCGR3, FCGR3A, IGFR3 / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: P08637

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Sugars , 3 types, 4 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.: 2
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)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 321 molecules

#6: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE CONFLICT VAL158 IS RELATED TO A NATURALLY OCCURRING VARIATION IN THE SEQUENCE OF HFCGIIIA

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.4 Sodium Malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011
RadiationMonochromator: Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→140.288 Å / Num. obs: 45955 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 33.4 Å2 / Rsym value: 0.126 / Net I/σ(I): 14.3
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 0.8264 % / Mean I/σ(I) obs: 1.04 / Num. unique all: 2392 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0112refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→140.288 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.919 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25173 2158 5 %RANDOM
Rwork0.19516 ---
all0.19858 40758 --
obs0.19794 40758 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.346 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---1.25 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.2→140.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 294 320 5443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025295
X-RAY DIFFRACTIONr_angle_refined_deg1.7772.0227247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5524.796221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70815826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2081518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213877
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 154 -
Rwork0.28 2751 -
obs--99.97 %
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)
11.3436-0.2361-0.34690.5244-0.03730.51110.110.04610.1928-0.0602-0.05050.0415-0.04160.0442-0.05950.06270.0050.03150.01090.00070.0497-17.65142.488517.2533
20.90590.4483-0.51851.4464-0.36620.42910.0432-0.0102-0.0772-0.0047-0.0175-0.1050.00570.0652-0.02560.0119-0.0025-0.02170.131-0.02170.05713.7879-14.561619.0249
30.2901-0.07280.00392.3806-0.29330.56180.02870.0062-0.0497-0.0661-0.12970.02740.007-0.0250.1010.02100.00520.0135-0.01440.0374-31.1858-45.029818.4464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A226 - 444
2X-RAY DIFFRACTION2B227 - 443
3X-RAY DIFFRACTION3C6 - 174

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