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- PDB-6wol: Next generation monomeric IgG4 Fc bound to neonatal Fc receptor -

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Basic information

Entry
Database: PDB / ID: 6wol
TitleNext generation monomeric IgG4 Fc bound to neonatal Fc receptor
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • IgG receptor FcRn large subunit p51
  • Immunoglobulin heavy constant gamma 4
KeywordsIMMUNE SYSTEM / antibody constant region / fragment crystallizable / mutated / neonatal Fc receptor
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / beta-2-microglobulin binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / beta-2-microglobulin binding / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Regulation of Complement cascade / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / Regulation of actin dynamics for phagocytic cup formation / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / Interleukin-4 and Interleukin-13 signaling / blood microparticle / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 4 / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsOganesyan, V.Y. / Shan, L. / van Dyk, N. / Dall'Acqua, W.F.
CitationJournal: Commun Biol / Year: 2021
Title: In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance.
Authors: Shan, L. / Dyk, N.V. / Haskins, N. / Cook, K.M. / Rosenthal, K.L. / Mazor, R. / Dragulin-Otto, S. / Jiang, Y. / Wu, H. / Dall'Acqua, W.F. / Borrok, M.J. / Damschroder, M.M. / Oganesyan, V.
History
DepositionApr 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Immunoglobulin heavy constant gamma 4
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6864
Polymers65,2223
Non-polymers1,4631
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint13 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.284, 122.598, 178.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23753.797 Da / Num. of mol.: 1 / Fragment: domains Ch3 and Ch4
Mutation: L351F, S354E, T366R, P395K, F405R, Y407E, L432C, H433S, N434Y, Y436L, T437C, Q438 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / Production host: Homo sapiens (human) / References: UniProt: P01861
#2: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 29720.383 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Homo sapiens (human) / References: UniProt: P55899
#3: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / References: UniProt: P61769
#4: 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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-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][a1221m-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_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]{}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 0.2 M magnesium chloride hexahydrate, 1 M sodium iodide, 0.1 M MES, pH 6 and 20% PEG 6000 at a protein concentration of 6.35 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.49→36.1 Å / Num. obs: 26347 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.086 / Net I/σ(I): 4.9
Reflection shellResolution: 2.49→2.6 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2798 / CC1/2: 0.757 / Rpim(I) all: 0.374

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hvw

5hvw


Resolution: 2.49→36.1 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.882 / SU B: 11.398 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.295
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 1032 3.9 %RANDOM
Rwork0.234 ---
obs0.2353 25263 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.71 Å2 / Biso mean: 45.346 Å2 / Biso min: 6.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å20 Å2-0 Å2
2--5.1 Å2-0 Å2
3----2.15 Å2
Refinement stepCycle: final / Resolution: 2.49→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 99 33 4708
Biso mean--79.23 33.17 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134819
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174270
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6796560
X-RAY DIFFRACTIONr_angle_other_deg1.1121.6019997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8515569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96422.782248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37715781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2271525
X-RAY DIFFRACTIONr_chiral_restr0.0540.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021007
LS refinement shellResolution: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 73 -
Rwork0.364 1658 -
all-1731 -
obs--89.92 %

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