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- PDB-1fc2: Crystallographic Refinement and Atomic Models of a Human FC Fragm... -

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Entry
Database: PDB / ID: 1fc2
TitleCrystallographic Refinement and Atomic Models of a Human FC Fragment and its Complex with Fragment B of Protein A from Staphylococcus Aureus at 2.9-and 2.8-Angstroms Resolution
Components
  • FRAGMENT B OF PROTEIN A COMPLEX
  • IMMUNOGLOBULIN FC
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Immunoglobulin heavy constant gamma 1 / Immunoglobulin G-binding protein A / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsDeisenhofer, J.
Citation
Journal: Biochemistry / Year: 1981
Title: Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution.
Authors: Deisenhofer, J.
#1: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1978
Title: Crystallization, Crystal Structure Analysis and Atomic Model of the Complex Formed by a Human Fc Fragment and Fragment B of Protein a from Staphylococcus Aureus
Authors: Deisenhofer, J. / Jones, T.A. / Huber, R. / Sjodahl, J. / Sjoquist, J.
History
DepositionMay 21, 1981Processing site: BNL
Revision 1.0Oct 2, 1981Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 16, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: FRAGMENT B OF PROTEIN A COMPLEX
D: IMMUNOGLOBULIN FC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5664
Polymers31,8452
Non-polymers1,7222
Water00
1
C: FRAGMENT B OF PROTEIN A COMPLEX
D: IMMUNOGLOBULIN FC
hetero molecules

C: FRAGMENT B OF PROTEIN A COMPLEX
D: IMMUNOGLOBULIN FC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1338
Polymers63,6904
Non-polymers3,4434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)70.600, 70.600, 147.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: THESE ATOMS WERE NOT FOUND IN THE ELECTRON DENSITY MAP. THEIR COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA
2: RESIDUE PRO D 374 IS A CIS-PROLINE.
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, FOR WHICH COORDINATES ARE PRESENTED BELOW, CONSISTS OF ONE FRAGMENT B OF PROTEIN A (CHAIN INDICATOR C BELOW) AND ONE-HALF OF AN FC FRAGMENT (CHAIN INDICATOR D BELOW) TOGETHER WITH ITS POLYSACCHARIDE. THE FOLLOWING SYMMETRY OPERATION WHEN APPLIED TO THE COORDINATES OF THE ONE-HALF OF THE FC FRAGMENT GIVEN BELOW (CHAIN D) WILL GENERATE THE SECOND HALF OF THE FC FRAGMENT MOLECULE TRNSF1 1 -0.50000 -0.86603 0.00000 0.000 TRNSF2 1 -0.86603 0.50000 0.00000 0.000 TRNSF3 1 0.00000 0.00000 -1.00000 49.133

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Components

#1: Protein FRAGMENT B OF PROTEIN A COMPLEX


Mass: 6608.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / References: UniProt: P02976, UniProt: P38507*PLUS
#2: Protein IMMUNOGLOBULIN FC


Mass: 25236.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: EMBL: Y14737, UniProt: P01857*PLUS
#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)]alpha-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
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-2-1-2-1-3-4/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)][a-D-6-deoxy-Altp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal grow
*PLUS
pH: 6.8 / Method: microdialysis / Details: took Deisenhofer et al., 1976a from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %protein1drop
20.5 M1dropNaCl
30.03 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 7002 / % possible obs: 62 % / Num. measured all: 25876

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Processing

RefinementHighest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 115 0 2125
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / Num. reflection all: 6243 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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