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- PDB-4n0u: Ternary complex between Neonatal Fc receptor, serum albumin and Fc -

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Basic information

Entry
Database: PDB / ID: 4n0u
TitleTernary complex between Neonatal Fc receptor, serum albumin and Fc
Components
  • Beta-2-microglobulin
  • Ig gamma-1 chain C region
  • IgG receptor FcRn large subunit p51
  • Serum albumin
KeywordsDNA BINDING PROTEIN / alpha/beta
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / Fc-gamma receptor I complex binding / Ciprofloxacin ADME / complement-dependent cytotoxicity / exogenous protein binding / cellular response to calcium ion starvation / IgG immunoglobulin complex / enterobactin binding / antibody-dependent cellular cytotoxicity / Heme biosynthesis ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / Fc-gamma receptor I complex binding / Ciprofloxacin ADME / complement-dependent cytotoxicity / exogenous protein binding / cellular response to calcium ion starvation / IgG immunoglobulin complex / enterobactin binding / antibody-dependent cellular cytotoxicity / Heme biosynthesis / HDL remodeling / IgG binding / negative regulation of mitochondrial depolarization / immunoglobulin receptor binding / immunoglobulin complex, circulating / Prednisone ADME / Classical antibody-mediated complement activation / Heme degradation / Initial triggering of complement / Aspirin ADME / beta-2-microglobulin binding / antioxidant activity / FCGR activation / toxic substance binding / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / Recycling of bile acids and salts / antigen binding / FCGR3A-mediated IL10 synthesis / : / : / platelet alpha granule lumen / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to starvation / Regulation of Complement cascade / fatty acid binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Post-translational protein phosphorylation / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / Regulation of actin dynamics for phagocytic cup formation / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / pyridoxal phosphate binding / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Platelet degranulation / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / Interleukin-4 and Interleukin-13 signaling
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Albumin / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsOganesyan, V. / Wu, H. / Dall'Acqua, W.F.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Insights into Neonatal Fc Receptor-based Recycling Mechanisms.
Authors: Oganesyan, V. / Damschroder, M.M. / Cook, K.E. / Li, Q. / Gao, C. / Wu, H. / Dall'acqua, W.F.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _pdbx_struct_assembly.oligomeric_count ..._chem_comp.type / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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 / _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 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
D: Serum albumin
E: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7955
Polymers131,3324
Non-polymers1,4631
Water00
1
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
D: Serum albumin
E: Ig gamma-1 chain C region
hetero molecules

A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
D: Serum albumin
E: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,59110
Polymers262,6648
Non-polymers2,9272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Unit cell
Length a, b, c (Å)153.190, 153.190, 145.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: FcRn, alpha chain, ecd, unp residue 27-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Escherichia coli (E. coli) / References: UniProt: P55899
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: beta-2 microglobulin, unp residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein Serum albumin


Mass: 66385.055 Da / Num. of mol.: 1 / Fragment: serum albumin, unp residue 27-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Escherichia coli (E. coli) / References: UniProt: P02768
#4: Protein Ig gamma-1 chain C region


Mass: 23765.738 Da / Num. of mol.: 1 / Fragment: IgG1 Fc, unp reisdues 119-327 / Mutation: M252Y, S254T, T256E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01857
#5: 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
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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: 4% Tacsimate, pH 4.0, 12% PEG 3350, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2012 / Details: Compound Parabolic Refractive X-ray Lenses
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→40 Å / Num. all: 17596 / Num. obs: 17420 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 180.947 / SU ML: 1.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.915 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30331 281 1.7 %RANDOM
Rwork0.28199 ---
obs0.28235 15915 91.33 %-
all-17596 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 143.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2---1.85 Å20 Å2
3---3.71 Å2
Refinement stepCycle: LAST / Resolution: 3.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9222 0 99 0 9321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.029578
X-RAY DIFFRACTIONr_bond_other_d0.0030.026625
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.97412998
X-RAY DIFFRACTIONr_angle_other_deg1.1973.00516106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14651151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43424.564447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.548151645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4651547
X-RAY DIFFRACTIONr_chiral_restr0.0680.21421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110494
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021898
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 21 -
Rwork0.448 903 -
obs--78.64 %
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)
14.10861.64440.47866.65620.76913.2212-0.17671.1355-0.5261-1.45830.5420.75940.4409-1.0119-0.36530.8773-0.0155-0.07751.46480.10740.702212.0002-37.794212.7316
27.6859-0.2136-0.995110.33931.58844.8651-0.04841.06120.6698-1.75230.3847-0.8953-0.5623-0.368-0.33631.1110.02550.81270.5208-0.11720.875951.1773-29.22661.1967
39.5581-0.374.958324.46272.47713.9602-1.0951-0.99941.61790.66032.0848-3.993-0.9270.4196-0.98970.7641-0.00710.62940.9659-1.14292.647162.3546-19.222812.7622
42.63221.36970.38358.6994-0.61381.66960.1866-0.17080.7739-0.0373-0.01-1.236-0.51470.2996-0.17660.5116-0.12820.49650.4955-0.48431.163678.5779-56.533.3747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D3 - 585
2X-RAY DIFFRACTION2A4 - 267
3X-RAY DIFFRACTION3B1 - 99
4X-RAY DIFFRACTION4E236 - 444

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