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- PDB-6wna: Next generation monomeric IgG4 Fc -

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Basic information

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


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG immunoglobulin complex / IgG binding / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / beta-2-microglobulin binding / FCGR activation / complement activation, classical pathway ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG immunoglobulin complex / IgG binding / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / beta-2-microglobulin binding / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / negative regulation of receptor binding / Regulation of Complement cascade / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / Regulation of actin dynamics for phagocytic cup formation / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / Interleukin-4 and Interleukin-13 signaling / protein homotetramerization / blood microparticle / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
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. ...: / 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: 2.4 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 22, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,5954
Polymers64,9703
Non-polymers1,6251
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint22 kcal/mol
Surface area29270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.095, 122.096, 179.446
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 IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 29433.115 Da / Num. of mol.: 1 / Fragment: extracellular region
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
#2: Protein 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
#3: Protein Immunoglobulin heavy constant gamma 4 / Ig gamma-4 chain C region


Mass: 23788.668 Da / Num. of mol.: 1 / Fragment: domains Ch2 and Ch3
Mutation: M252Y, S254T, T256E, L351F, S354E, T366R, P395K, F405R, Y407E,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / Production host: Homo sapiens (human) / References: UniProt: P01861
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.2 M magnesium chloride hexahydrate, 30% 1,5-diaminopentane dihydrochloride, 0.1 M MES, pH 6 and 20% PEG 6000 at a protein concentration of 6 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: 1.195 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 29521 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3072 / CC1/2: 0.631 / Rpim(I) all: 0.519 / % possible all: 99.5

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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, 4n0u

5hvw

4n0u


Resolution: 2.4→35 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.142 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.26
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 876 3 %RANDOM
Rwork0.2139 ---
obs0.2154 28605 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.86 Å2 / Biso mean: 45.394 Å2 / Biso min: 15.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å2-0 Å20 Å2
2--2.9 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 110 88 4728
Biso mean--85.07 34.47 -
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134787
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174228
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.6856512
X-RAY DIFFRACTIONr_angle_other_deg1.1521.6049896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8235558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5322.76250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12615768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7011525
X-RAY DIFFRACTIONr_chiral_restr0.060.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021005
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 77 -
Rwork0.323 2051 -
all-2128 -
obs--99.44 %

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