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- PDB-1fc1: CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF A HUMAN FC FRAGM... -

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Entry
Database: PDB / ID: 1fc1
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
ComponentsFC FRAGMENT
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / 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 / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 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: 1976
Title: Crystallographic Structural Studies of a Human Fc Fragment. II. A Complete Model Based on a Fourier Map at 3.5 Angstroms Resolution
Authors: Deisenhofer, J. / Colman, P.M. / Epp, O. / Huber, R.
#2: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1976
Title: Crystallographic Structural Studies of a Human Fc-Fragment. I. An Electron-Density Map at 4 Angstroms Resolution and a Partial Model
Authors: Deisenhofer, J. / Colman, P.M. / Huber, R. / Haupt, H. / Schwick, G.
#3: Journal: FEBS Lett. / Year: 1974
Title: X-Ray Studies on Antibody Fragments
Authors: Colman, P.M. / Epp, O. / Fehlhammer, H. / Bode, W. / Schiffer, M. / Lattman, E.E. / Jones, T.A.
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: Non-polymer description / 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_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FC FRAGMENT
B: FC FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7244
Polymers50,4732
Non-polymers3,2512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint57 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.400, 146.400, 50.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THESE ATOMS WERE NOT FOUND IN THE ELECTRON DENSITY MAP. THEIR COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA
2: RESIDUE 374 OF EACH CHAIN IS A CIS-PROLINE.
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS ONE FC FRAGMENT WHICH CONSISTS OF TWO CHEMICALLY IDENTICAL POLYPEPTIDE CHAINS EACH WITH ATTACHED POLYSACCHARIDE. THESE TWO CHAINS ARE DESIGNATED CHAIN 1 AND CHAIN 2 BY THE DEPOSITOR AND REPRESENTED WITH CHAIN IDENTIFIERS A AND B BELOW. THE CH2 AND CH3 DOMAINS OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT POLYPEPTIDE CHAINS ARE RELATED BY NON-CRYSTALLOGRAPHIC (APPROXIMATE) DIADS (SEE JRNL REFERENCE ABOVE FOR A COMPLETE DISCUSSION). THE FOLLOWING TRANSFORMATION, WHEN APPLIED TO THE CH2 DOMAIN OF CHAIN A (RESIDUES PRO A 238 THROUGH GLY A 341 TOGETHER WITH THE POLYSACCHARIDE), WILL YIELD APPROXIMATE COORDINATES FOR THE CH2 DOMAIN OF CHAIN B (RESIDUES PRO B 238 THROUGH GLY B 341 TOGETHER WITH THE POLYSACCHARIDE). TRNSF1 1 -0.99391 -0.03853 -0.10322 92.070 TRNSF2 1 -0.06679 0.95579 0.28635 -0.310 TRNSF3 1 0.08759 0.29136 -0.95207 11.160 THE FOLLOWING TRANSFORMATION, WHEN APPLIED TO THE CH3 DOMAIN OF CHAIN A (RESIDUES GLN A 342 THROUGH LEU A 443), WILL YIELD APPROXIMATE COORDINATES FOR THE CH3 DOMAIN OF CHAIN B (RESIDUES GLN B 342 THROUGH LEU B 443). TRNSF1 2 -0.99907 -0.03950 -0.01721 88.510 TRNSF2 2 -0.04232 0.97468 0.21956 -1.010 TRNSF3 2 0.00810 0.22008 -0.97544 24.570

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Components

#1: Protein FC FRAGMENT


Mass: 25236.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P01857
#2: 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.: 2
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.1 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 220 0 3532

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