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- PDB-4byh: Crystal structure of sialylated IgG Fc -

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Basic information

Entry
Database: PDB / ID: 4byh
TitleCrystal structure of sialylated IgG Fc
ComponentsIG GAMMA-1 CHAIN C REGION
KeywordsIMMUNE SYSTEM / ANTIBODY / SIALYATION / IMMUNOGLOBULIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCrispin, M. / Yu, X. / Bowden, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal Structure of Sialylated Igg Fc: Implications for the Mechanism of Intravenous Immunoglobulin Therapy.
Authors: Crispin, M. / Yu, X. / Bowden, T.A.
History
DepositionJul 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_special_symmetry / pdbx_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 23, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / struct_conn
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_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _chem_comp.pdbx_synonyms / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_special_symmetry.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 13, 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: IG GAMMA-1 CHAIN C REGION
B: IG GAMMA-1 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4876
Polymers52,7122
Non-polymers3,7754
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint46 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.000, 153.000, 111.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21B-501-

CL

31A-649-

HOH

41A-651-

HOH

51B-633-

HOH

61B-692-

HOH

71B-699-

HOH

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Components

#1: Protein IG GAMMA-1 CHAIN C REGION / IGG FC


Mass: 26355.787 Da / Num. of mol.: 2 / Fragment: RESIDUES 106-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1916.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5-6/a4-b1_a6-j1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1_h6-i2WURCSPDB2Glycan 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+2)][a-D-Neup5Ac]{}}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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-(1-3)-[beta-D-galactopyranose-(1-4)-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: 1787.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-4-3-1-4-5/a4-b1_a6-j1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1_h4-i1WURCSPDB2Glycan 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]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
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: 4.01 Å3/Da / Density % sol: 69.3 % / Description: NONE
Crystal growpH: 4 / Details: 4M NACL, 0.1 M CITRATE PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2013 / Details: MIRRORS
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→66 Å / Num. obs: 34456 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AVE

3ave


Resolution: 2.3→66.34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.852 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26165 1745 5.1 %RANDOM
Rwork0.22223 ---
obs0.22426 32683 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.114 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-1.67 Å20 Å2
2---1.67 Å20 Å2
3---5.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→66.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 253 166 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193733
X-RAY DIFFRACTIONr_bond_other_d0.0040.023422
X-RAY DIFFRACTIONr_angle_refined_deg1.5012.0375122
X-RAY DIFFRACTIONr_angle_other_deg1.1593.0027906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43124.968155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03315593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3121513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213931
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02767
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_it1.8233.0381675
X-RAY DIFFRACTIONr_mcbond_other1.8223.0371674
X-RAY DIFFRACTIONr_mcangle_it3.1544.5432094
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3323.7722057
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 121 -
Rwork0.351 2390 -
obs--99.48 %
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)
119.45267.6082-9.37283.1303-3.60894.57630.2662-2.01120.7144-0.0341-0.28660.33710.00831.0410.02040.2741-0.17320.12490.8705-0.14370.7226116.246542.15119.1499
23.748-0.18350.26614.89070.05350.0246-0.3576-0.0154-0.12840.11270.5217-1.1743-0.01420.0023-0.16410.1592-0.02880.03890.1809-0.31570.9096111.62948.5557121.2402
30.6495-0.2417-0.25094.5317-1.16420.4848-0.149-0.0764-0.1030.12840.18120.5538-0.032-0.0202-0.03220.25570.0480.01790.2163-0.0360.581585.852527.7418121.4155
46.92285.65362.23346.24511.72690.8224-0.10820.12750.4466-0.01530.11430.915-0.18350.107-0.00610.403-0.00410.1150.3041-0.0140.3539114.358512.6459113.8047
51.23441.1718-0.54412.0956-0.63520.34940.03470.0038-0.1850.0352-0.0107-0.0279-0.04530.1419-0.0240.3703-0.01540.03880.3472-0.00550.2714127.143714.9853116.5051
61.2645-1.46691.25435.0722-1.9121.33220.2673-0.1996-0.0214-0.8616-0.21020.57020.3831-0.0867-0.05710.47470.0449-0.01280.2168-0.04370.493590.477813.3527114.2194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A238 - 243
2X-RAY DIFFRACTION2A244 - 338
3X-RAY DIFFRACTION3A339 - 444
4X-RAY DIFFRACTION4B237 - 258
5X-RAY DIFFRACTION5B259 - 339
6X-RAY DIFFRACTION6B340 - 444

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