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- PDB-4hag: Crystal structure of fc-fragment of human IgG2 antibody (centered... -

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Basic information

Entry
Database: PDB / ID: 4hag
TitleCrystal structure of fc-fragment of human IgG2 antibody (centered crystal form)
ComponentsIg gamma-2 chain C region
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


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 / antigen binding ...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 / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / adaptive immune response / blood microparticle / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTeplyakov, A. / Malia, T. / Obmolova, G. / Zhao, Y. / Gilliland, G.
CitationJournal: Mol.Immunol. / Year: 2013
Title: IgG2 Fc structure and the dynamic features of the IgG CH2-CH3 interface.
Authors: Teplyakov, A. / Zhao, Y. / Malia, T.J. / Obmolova, G. / Gilliland, G.L.
History
DepositionSep 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Derived calculations
Revision 1.2Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-2 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4302
Polymers25,1121
Non-polymers1,3171
Water0
1
A: Ig gamma-2 chain C region
hetero molecules

A: Ig gamma-2 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8594
Polymers50,2252
Non-polymers2,6342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6910 Å2
ΔGint48 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.240, 144.400, 75.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ig gamma-2 chain C region


Mass: 25112.469 Da / Num. of mol.: 1 / Fragment: CH2, CH3 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG2 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P01859
#2: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1317.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_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]{}}}}}}LINUCSPDB-CARE
Sequence detailsTHERE IS A SER -> ALA SEQUENCE CONFLICT AT RESIDUE 257 IN UNIPROT DATABASE.

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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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG 3350, 0.1 M HEPES. CRYO CONDITIONS: 23% PEG 3350, 0.1 M HEPES, 22% GLYCEROL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 6, 2009 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. all: 3896 / Num. obs: 3896 / % possible obs: 94 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.3
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.1 / % possible all: 60.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ave

3ave


Resolution: 3.4→15 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.827 / SU B: 134.319 / SU ML: 0.854 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.836 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3493 176 4.6 %RANDOM
Rwork0.29896 ---
all0.30108 3671 --
obs0.30108 3671 89.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 193.5 Å2
Baniso -1Baniso -2Baniso -3
1--15.34 Å20 Å20 Å2
2--23.47 Å20 Å2
3----8.12 Å2
Refinement stepCycle: LAST / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 89 0 1753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221808
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.0132472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42125.06577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76215292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.113156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0221326
LS refinement shellResolution: 3.4→3.492 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 9 -
Rwork0.467 167 -
obs--60.5 %
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)
16.84260.17951.184615.48462.388214.6557-1.4561.80183.6222-0.23110.52231.039-3.6539-0.47960.93361.7459-0.3173-0.63461.2110.8682.344714.648224.75317.3166
241.885.31272.34477.40251.50979.6428-0.45644.5991-3.552-0.1225-0.42130.24680.51430.83190.87770.61150.06490.18830.5996-0.44110.56195.0699-6.070512.1143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A501 - 507
2X-RAY DIFFRACTION1A237 - 340
3X-RAY DIFFRACTION2A341 - 444

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