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- PDB-7q15: Crystal structure of FcRn and beta-2-microglobulin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7q15
TitleCrystal structure of FcRn and beta-2-microglobulin in complex with IgG1-Fc-MST-HN (efgartigimod)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • IgG receptor FcRn large subunit p51
  • IgG1-Fc-MST-HN
KeywordsIMMUNE SYSTEM / Neonatal Fc Receptor FcRn / FcRn / Fc / IgG1-Fc-MST-HN / efgartigimod / ARGX-113 / FcRn-binding protein
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / 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 ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / 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 / 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. / 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
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsPannecoucke, E. / Savvides, S.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: The Fab region of IgG impairs the internalization pathway of FcRn upon Fc engagement.
Authors: Brinkhaus, M. / Pannecoucke, E. / van der Kooi, E.J. / Bentlage, A.E.H. / Derksen, N.I.L. / Andries, J. / Balbino, B. / Sips, M. / Ulrichts, P. / Verheesen, P. / de Haard, H. / Rispens, T. / ...Authors: Brinkhaus, M. / Pannecoucke, E. / van der Kooi, E.J. / Bentlage, A.E.H. / Derksen, N.I.L. / Andries, J. / Balbino, B. / Sips, M. / Ulrichts, P. / Verheesen, P. / de Haard, H. / Rispens, T. / Savvides, S.N. / Vidarsson, G.
History
DepositionOct 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: 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
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
E: IgG1-Fc-MST-HN
F: IgG1-Fc-MST-HN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,9508
Polymers152,9026
Non-polymers3,0482
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Multi-angle laser-light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-1 kcal/mol
Surface area53490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.429, 53.107, 195.745
Angle α, β, γ (deg.)90, 92.18, 90
Int Tables number4
Space group name H-MP1211

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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: 37225.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Variant (production host): MGAT-/- TR+ / References: UniProt: P55899
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 13732.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Variant (production host): MGAT-/- TR+ / References: UniProt: P61769
#3: Antibody IgG1-Fc-MST-HN


Mass: 25492.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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-ROHGlycam 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
[][D-1-deoxy-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: 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)-[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: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-4-3-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Sodium Cacodylate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.89 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.146→48.901 Å / Num. obs: 21510 / % possible obs: 90.4 % / Redundancy: 3.1 % / CC1/2: 0.942 / Rrim(I) all: 0.38 / Net I/σ(I): 4.2
Reflection shellResolution: 3.146→3.449 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1073 / CC1/2: 0.265 / Rrim(I) all: 0.0156

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0U

1n0u


Resolution: 3.301→48.9 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.805 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.578
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1003 -RANDOM
Rwork0.2063 ---
obs0.2077 18236 66.7 %-
Displacement parametersBiso mean: 63.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.7863 Å20 Å21.7683 Å2
2---0.2801 Å20 Å2
3---3.0664 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 3.301→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8310 0 206 0 8516
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0058798HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8112122HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2645SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1476HARMONIC5
X-RAY DIFFRACTIONt_it8575HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1224SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact5561SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion16.98
LS refinement shellResolution: 3.301→3.49 Å
RfactorNum. reflection% reflection
Rfree0.2424 23 -
Rwork0.2329 --
obs--8.68 %
Refinement TLS params.

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)
13.40320.22320.64940.2674-0.30670.3283-0.1192-0.0159-0.2391-0.01590.1357-0.0393-0.2391-0.0393-0.0165-0.3079-0.01310.04360.0364-0.05680.1235-20.0999-43.2579-8.3446
23.5353-2.89270.29453.9839-0.22921.2669-0.2977-0.2435-0.2421-0.24350.21270.0275-0.24210.02750.0851-0.31350.00280.1141-0.0375-0.120.2495-9.8232-51.6318-20.8746
31.10.5028-1.45050.6799-0.72043.19020.2189-0.2074-0.2543-0.20740.1447-0.167-0.2543-0.167-0.36360.31160.0402-0.0905-0.29840.0439-0.2248-48.611327.0497-77.4978
41.9121.9351-2.39164.0241-0.64265.21350.2595-0.0892-0.4163-0.08920.04580.5336-0.41630.5336-0.30540.2984-0.14610.084-0.27260.0964-0.2984-33.0235.6752-75.9643
52.0541-1.07710.49770.4958-0.02110.52530.0321-0.43520.0213-0.43520.0660.05640.02130.0564-0.09820.0431-0.07410.098-0.1534-0.01940.1092-31.7031-19.4508-37.0128
61.31940.9676-1.08731.0792-0.78232.1188-0.1251-0.32570.0872-0.32570.10470.21670.08720.21670.02040.12870.082-0.0005-0.2014-0.0107-0.0492-37.94743.2481-49.9231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 270
2X-RAY DIFFRACTION2{ B|* }B1 - 99
3X-RAY DIFFRACTION3{ C|* }C5 - 268
4X-RAY DIFFRACTION4{ D|* }D1 - 98
5X-RAY DIFFRACTION5{ E|* }E236 - 444
6X-RAY DIFFRACTION5{ E|* }E445 - 453
7X-RAY DIFFRACTION6{ F|* }F238 - 444
8X-RAY DIFFRACTION6{ F|* }F445 - 453

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