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- PDB-5w5n: Crystal structure of human IgG4-Sigma2 Fc fragment -

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Basic information

Entry
Database: PDB / ID: 5w5n
TitleCrystal structure of human IgG4-Sigma2 Fc fragment
ComponentsImmunoglobulin heavy constant gamma 4
KeywordsIMMUNE SYSTEM / FC / 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 / Interleukin-4 and Interleukin-13 signaling / 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
ACETATE ION / Immunoglobulin heavy constant gamma 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsArmstrong, A.A. / Gilliland, G.L.
CitationJournal: Antibodies / Year: 2017
Title: Functional, Biophysical, and Structural Characterization of Human IgG1 and IgG4 Fc Variants with Ablated Immune Functionality.
Authors: Tam, S.H. / McCarthy, S.G. / Armstrong, A.A. / Somani, S. / Wu, S.J. / Liu, X. / Gervais, A. / Ernst, R. / Saro, D. / Decker, R. / Luo, J. / Gilliland, G.L. / Chiu, M.L. / Scallon, B.J.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy constant gamma 4
B: Immunoglobulin heavy constant gamma 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2947
Polymers49,9462
Non-polymers3,3485
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint59 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.520, 78.470, 97.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Immunoglobulin heavy constant gamma 4 / Ig gamma-4 chain C region


Mass: 24973.119 Da / Num. of mol.: 2 / Fragment: Sigma2 Fc fragment, UNP residues 106-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P01861

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Sugars , 2 types, 2 molecules

#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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1479.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_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]{}}}}}}}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-(1-6)-[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
DGalpb1-4DGlcpNAcb1-2DManpa1-6[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-1b_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)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 270 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 20K, 0.1 M sodium acetate, 5.5, 5% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→47.264 Å / Num. obs: 49481 / % possible obs: 99.9 % / Redundancy: 7.35 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.82
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7.42 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 3648 / CC1/2: 0.906 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1428refinement
XDSdata reduction
XDSdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.264 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2154 2525 5.1 %
Rwork0.181 --
obs0.1827 49469 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 226 267 3779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183751
X-RAY DIFFRACTIONf_angle_d1.6995147
X-RAY DIFFRACTIONf_dihedral_angle_d14.1231427
X-RAY DIFFRACTIONf_chiral_restr0.124617
X-RAY DIFFRACTIONf_plane_restr0.009639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88560.30051410.26392575X-RAY DIFFRACTION100
1.8856-1.92410.22921450.22222581X-RAY DIFFRACTION100
1.9241-1.96590.25921470.21582571X-RAY DIFFRACTION100
1.9659-2.01160.28951410.21152568X-RAY DIFFRACTION100
2.0116-2.06190.22511310.20662570X-RAY DIFFRACTION100
2.0619-2.11770.2491310.19382616X-RAY DIFFRACTION100
2.1177-2.180.23581500.19862544X-RAY DIFFRACTION100
2.18-2.25040.27081300.19942599X-RAY DIFFRACTION100
2.2504-2.33080.25331450.20972567X-RAY DIFFRACTION100
2.3308-2.42410.28331260.21172600X-RAY DIFFRACTION100
2.4241-2.53440.25471430.20672606X-RAY DIFFRACTION100
2.5344-2.6680.24011560.19912598X-RAY DIFFRACTION100
2.668-2.83520.24511580.19492577X-RAY DIFFRACTION100
2.8352-3.05410.23271380.18862621X-RAY DIFFRACTION100
3.0541-3.36130.23081260.18092637X-RAY DIFFRACTION100
3.3613-3.84750.17921390.16582646X-RAY DIFFRACTION100
3.8475-4.84670.17231330.14132676X-RAY DIFFRACTION100
4.8467-47.27940.17881450.17152792X-RAY DIFFRACTION100

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