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- PDB-3m1b: Crystal structure of human FcRn with a dimeric peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 3m1b
TitleCrystal structure of human FcRn with a dimeric peptide inhibitor
Components
  • Beta-2-microglobulin
  • DIMERIC PEPTIDE INHIBITOR
  • IgG receptor FcRn large subunit p51
KeywordsIMMUNE SYSTEM/INHIBITOR / IMMUNOGLOBULIN BINDING PROTEIN / Cell membrane / Disulfide bond / Glycoprotein / IgG-binding protein / Immunoglobulin domain / Membrane / Receptor / Transmembrane / Amyloid / Amyloidosis / Disease mutation / Glycation / Immune response / MHC I / Pyrrolidone carboxylic acid / Secreted / IMMUNE SYSTEM-IMMUNE SYSTEM INHIBITOR / IMMUNE SYSTEM-INHIBITOR complex
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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / : / : / 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 iron ion / Endosomal/Vacuolar pathway / 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 / 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 / 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 / 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 / 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 / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal 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
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 ...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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DIMERIC PEPTIDE INHIBITOR / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMezo, A.R. / Sridhar, V. / Badger, J. / Sakorafas, P. / Nienaber, V.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: X-ray crystal structures of monomeric and dimeric peptide inhibitors in complex with the human neonatal Fc receptor, FcRn.
Authors: Mezo, A.R. / Sridhar, V. / Badger, J. / Sakorafas, P. / Nienaber, V.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Derived calculations
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4May 4, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
G: IgG receptor FcRn large subunit p51
H: Beta-2-microglobulin
I: DIMERIC PEPTIDE INHIBITOR
J: DIMERIC PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)169,21210
Polymers169,21210
Non-polymers00
Water00
1
A: IgG receptor FcRn large subunit p51


Theoretical massNumber of molelcules
Total (without water)29,7201
Polymers29,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,7481
Polymers11,7481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IgG receptor FcRn large subunit p51


Theoretical massNumber of molelcules
Total (without water)29,7201
Polymers29,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,7481
Polymers11,7481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: IgG receptor FcRn large subunit p51


Theoretical massNumber of molelcules
Total (without water)29,7201
Polymers29,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,7481
Polymers11,7481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: IgG receptor FcRn large subunit p51


Theoretical massNumber of molelcules
Total (without water)29,7201
Polymers29,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,7481
Polymers11,7481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: DIMERIC PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)1,6691
Polymers1,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: DIMERIC PEPTIDE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)1,6691
Polymers1,6691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.050, 158.431, 82.539
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
IgG receptor FcRn large subunit p51 / FcRn / Neonatal Fc receptor / IgG Fc fragment receptor transporter alpha chain


Mass: 29720.383 Da / Num. of mol.: 4 / Fragment: UNP residues 24-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Cell (production host): CHOK1SV cells / Production host: Cricetinae (hamsters) / References: UniProt: P55899
#2: Protein
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell (production host): CHOK1SV cells / Production host: Cricetinae (hamsters) / References: UniProt: P61769
#3: Protein/peptide DIMERIC PEPTIDE INHIBITOR


Type: Polypeptide / Class: Inhibitor / Mass: 1669.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: DIMERIC PEPTIDE INHIBITOR
Sequence detailsACE AT THE N-TERMINUS OF CHAIN I IS COVALENTLY BONDED WITH ACE AT THE N-TERMINUS OF CHAIN J

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 2ul protein:peptide with 2ul buffer containing 100 mM phosphate/citric acid, 22% PEG 1000 and 8% ethanol , pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDate: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 29051 / Num. obs: 29051 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4
Reflection shellResolution: 3.1→3.2 Å / % possible all: 58

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Processing

Software
NameClassification
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M17

3m17


Resolution: 3.1→37.24 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.802 / SU B: 50.517 / SU ML: 0.901 / Cross valid method: THROUGHOUT / ESU R Free: 0.793 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.39658 1475 5.1 %RANDOM
Rwork0.31386 ---
obs0.31803 27550 100 %-
all-27550 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.575 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å2-0.04 Å2
2--1.06 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11241 0 0 0 11241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02111602
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.94315857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48451454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20823.901523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.204151591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5051552
X-RAY DIFFRACTIONr_chiral_restr0.0770.21661
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029185
X-RAY DIFFRACTIONr_nbd_refined0.2270.25865
X-RAY DIFFRACTIONr_nbtor_refined0.3080.27619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2478
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.213
X-RAY DIFFRACTIONr_mcbond_it0.44527455
X-RAY DIFFRACTIONr_mcangle_it0.7882.511623
X-RAY DIFFRACTIONr_scbond_it0.54834852
X-RAY DIFFRACTIONr_scangle_it0.8924.54234
LS refinement shellResolution: 3.1→3.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 67 -
Rwork0.423 1113 -
obs--100 %

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