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- PDB-1e4k: CRYSTAL STRUCTURE OF SOLUBLE HUMAN IGG1 FC FRAGMENT-FC-GAMMA RECE... -

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Basic information

Entry
Database: PDB / ID: 1e4k
TitleCRYSTAL STRUCTURE OF SOLUBLE HUMAN IGG1 FC FRAGMENT-FC-GAMMA RECEPTOR III COMPLEX
Components
  • FC FRAGMENT OF HUMAN IGG1
  • LOW AFFINITY IMMUNOGLOBULIN GAMMA FC RECEPTOR III
KeywordsIMMUNE SYSTEM / FC FRAGMENT / IGG / RECEPTOR
Function / homology
Function and homology information


GPI anchor binding / IgG receptor activity / Post-translational modification: synthesis of GPI-anchored proteins / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / immunoglobulin receptor binding / Classical antibody-mediated complement activation ...GPI anchor binding / IgG receptor activity / Post-translational modification: synthesis of GPI-anchored proteins / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / immunoglobulin receptor binding / Classical antibody-mediated complement activation / immunoglobulin complex, circulating / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane / Neutrophil degranulation / 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 ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor III-B / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSondermann, P. / Huber, R. / Oosthuizen, V. / Jacob, U.
CitationJournal: Nature / Year: 2000
Title: The 3.2A Crystal Structure of the Human Igg1 Fc Fragment-Fc-Gamma-Riii Complex
Authors: Sondermann, P. / Huber, R. / Oosthuizen, V. / Jacob, U.
History
DepositionJul 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
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_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 / _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 2.1Dec 13, 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FC FRAGMENT OF HUMAN IGG1
B: FC FRAGMENT OF HUMAN IGG1
C: LOW AFFINITY IMMUNOGLOBULIN GAMMA FC RECEPTOR III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1045
Polymers70,8533
Non-polymers3,2512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-18.1 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.320, 115.320, 299.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(1), (1), (1)

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Components

#1: Protein FC FRAGMENT OF HUMAN IGG1 / IGG1-FC


Mass: 25365.795 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT / Source method: isolated from a natural source / Details: OBTAINED BY PLASMIN DIGESTION / Source: (natural) HOMO SAPIENS (human) / Secretion: BLOOD / References: UniProt: P01857
#2: Protein LOW AFFINITY IMMUNOGLOBULIN GAMMA FC RECEPTOR III / CD16


Mass: 20121.453 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: LEUKOCYTE / Plasmid: PET21 / Cellular location (production host): INCLUSION BODIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75015
#3: Polysaccharide alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...alpha-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_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)][a-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_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]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 66.8 %
Crystal growpH: 5.8
Details: 0.1M MES/TRIS PH 5.6, 0.2M K/NA TARTRATE, 6.0% PEG8000
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mMMops1drop
3150 mM1dropNaCl
40.02 %sodium azide1drop
5100 mMMES-Tris1reservoir
66 %(w/v)PEG80001reservoir
7200 mMK-Na tartrate1reservoir
80.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 18596 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.133
Reflection shellHighest resolution: 3.2 Å / % possible all: 66.8
Reflection shell
*PLUS
% possible obs: 66.8 % / Rmerge(I) obs: 0.607

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2FCB, 1FC1

2fcb

1fc1


Resolution: 3.2→100 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.3569 -5 %RANDOM
Rwork0.2708 ---
obs0.2708 18596 94.9 %-
Solvent computationSolvent model: DENSITY MODIFICATION
Displacement parametersBiso mean: 95.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.924 Å218.494 Å20 Å2
2---1.924 Å20 Å2
3---3.848 Å2
Refinement stepCycle: LAST / Resolution: 3.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 220 0 5042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.17
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN.PARAM
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM

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