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- PDB-5bjt: Crystal structure of human FcRn with a peptide inhibitor at multi... -

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Basic information

Entry
Database: PDB / ID: 5bjt
TitleCrystal structure of human FcRn with a peptide inhibitor at multiple sites
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • IgG receptor FcRn large subunit p51
  • peptide inhibitor
KeywordsIMMUNE SYSTEM/INHIBITOR / immunoglobulin binding protein / cell membrane / disulfide bond / glycoprotein / IgG-binding protein / immunoglobulin domain / receptor / transmembrane / amyloid / amyloidosis / disease mutation / glycation / immune response / MHC I / pyrrolidone carboxylic acid / secreted / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / early endosome lumen / positive regulation of receptor binding / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / 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 / endoplasmic reticulum lumen / external side of plasma membrane / 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
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 ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNienaber, V. / Badger, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Hepatic FcRn regulates albumin homeostasis and susceptibility to liver injury.
Authors: Pyzik, M. / Rath, T. / Kuo, T.T. / Win, S. / Baker, K. / Hubbard, J.J. / Grenha, R. / Gandhi, A. / Kramer, T.D. / Mezo, A.R. / Taylor, Z.S. / McDonnell, K. / Nienaber, V. / Andersen, J.T. / ...Authors: Pyzik, M. / Rath, T. / Kuo, T.T. / Win, S. / Baker, K. / Hubbard, J.J. / Grenha, R. / Gandhi, A. / Kramer, T.D. / Mezo, A.R. / Taylor, Z.S. / McDonnell, K. / Nienaber, V. / Andersen, J.T. / Mizoguchi, A. / Blumberg, L. / Purohit, S. / Jones, S.D. / Christianson, G. / Lencer, W.I. / Sandlie, I. / Kaplowitz, N. / Roopenian, D.C. / Blumberg, R.S.
History
DepositionOct 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
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
P: peptide inhibitor
Q: peptide inhibitor
R: peptide inhibitor
S: peptide inhibitor
T: peptide inhibitor
U: peptide inhibitor
V: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)180,98415
Polymers180,98415
Non-polymers00
Water0
1
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)41,4692
Polymers41,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-14 kcal/mol
Surface area17200 Å2
MethodPISA
2
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)41,4692
Polymers41,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-10 kcal/mol
Surface area17070 Å2
MethodPISA
3
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)41,4692
Polymers41,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-10 kcal/mol
Surface area17420 Å2
MethodPISA
4
G: IgG receptor FcRn large subunit p51
H: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)41,4692
Polymers41,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area18820 Å2
MethodPISA
5
P: peptide inhibitor


  • defined by author&software
  • 2.16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1600 Å2
MethodPISA
6
Q: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1720 Å2
MethodPISA
7
R: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1710 Å2
MethodPISA
8
S: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1530 Å2
MethodPISA
9
T: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1450 Å2
MethodPISA
10
U: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1540 Å2
MethodPISA
11
V: peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.917, 176.152, 245.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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: 29720.383 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 24-290)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P55899
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


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 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61769
#3: Protein/peptide
peptide inhibitor


Mass: 2158.483 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 1.6 M ammonium sulfate, 20% glycerol, 0.8 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2008
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 37736 / % possible obs: 99.9 % / Observed criterion σ(I): -4 / Redundancy: 5.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.5.0072refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M17

3m17


Resolution: 3.2→49.27 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.79 / SU B: 29.352 / SU ML: 0.52 / Cross valid method: THROUGHOUT / ESU R Free: 0.624
RfactorNum. reflection% reflectionSelection details
Rfree0.339 1885 5 %RANDOM
Rwork0.252 ---
obs0.257 35848 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 62.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11486 0 0 0 11486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02111859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.93116261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.61351545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43623.609496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.685151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9321546
X-RAY DIFFRACTIONr_chiral_restr0.1290.21730
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219444
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.97327751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.832.512125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84734108
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0954.54136
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: 3.2→3.29 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.504 129
Rwork0.295 2540

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