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- PDB-6c99: Crystal structure of FcRn bound to UCB-303 -

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Basic information

Entry
Database: PDB / ID: 6c99
TitleCrystal structure of FcRn bound to UCB-303
Components
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
KeywordsIMMUNE SYSTEM / Neonatal Fc Receptor / FcRn / Inhibitor / beta 2 microglobulin / b2m
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 / 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 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 / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / 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 / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / 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 / Golgi apparatus / endoplasmic reticulum / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-EQY / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFox III, D. / Abendroth, J. / Porter, J. / Deboves, H.
CitationJournal: PLoS Biol. / Year: 2018
Title: Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR.
Authors: Stoppler, D. / Macpherson, A. / Smith-Penzel, S. / Basse, N. / Lecomte, F. / Deboves, H. / Taylor, R.D. / Norman, T. / Porter, J. / Waters, L.C. / Westwood, M. / Cossins, B. / Cain, K. / ...Authors: Stoppler, D. / Macpherson, A. / Smith-Penzel, S. / Basse, N. / Lecomte, F. / Deboves, H. / Taylor, R.D. / Norman, T. / Porter, J. / Waters, L.C. / Westwood, M. / Cossins, B. / Cain, K. / White, J. / Griffin, R. / Prosser, C. / Kelm, S. / Sullivan, A.H. / Fox, D. / Carr, M.D. / Henry, A. / Taylor, R. / Meier, B.H. / Oschkinat, H. / Lawson, A.D.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 6, 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
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,92113
Polymers84,3134
Non-polymers1,6089
Water6,485360
1
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2059
Polymers42,1562
Non-polymers1,0497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-11 kcal/mol
Surface area16760 Å2
MethodPISA
2
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7164
Polymers42,1562
Non-polymers5592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-10 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.770, 76.080, 140.040
Angle α, β, γ (deg.)90.00, 93.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 30408.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P55899
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 368 molecules

#3: Chemical ChemComp-EQY / methyl 7-(3,5-difluorophenyl)-5-(pyridin-3-yl)[1,2,4]triazolo[1,5-a]pyrimidine-6-carboxylate


Mass: 367.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H11F2N5O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3
Details: APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM ...Details: APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.01-3.09 AND 12-16% W/V PEG 6,000. CRYSTALS OF FCRN WERE SOAKED FOR THREE DAYS IN BUFFER CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0, 20% W/V PEG6,000, AND 20% GLYCEROL AND 12.5MM UCB-303.
PH range: 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59144 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.96
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4319 / CC1/2: 0.837 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.13_2998: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.59 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.15
RfactorNum. reflection% reflection
Rfree0.2202 2887 4.88 %
Rwork0.189 --
obs0.1905 59131 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 111 360 5981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075889
X-RAY DIFFRACTIONf_angle_d0.9068075
X-RAY DIFFRACTIONf_dihedral_angle_d15.5843427
X-RAY DIFFRACTIONf_chiral_restr0.049853
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.03290.28271520.24622597X-RAY DIFFRACTION100
2.0329-2.0680.29431570.2422690X-RAY DIFFRACTION100
2.068-2.10560.27291500.22982627X-RAY DIFFRACTION100
2.1056-2.14610.26811160.22662659X-RAY DIFFRACTION100
2.1461-2.18990.25241420.22562716X-RAY DIFFRACTION100
2.1899-2.23750.29831210.21642635X-RAY DIFFRACTION100
2.2375-2.28950.28961300.21382710X-RAY DIFFRACTION100
2.2895-2.34680.27961210.212678X-RAY DIFFRACTION100
2.3468-2.41020.27341500.21462655X-RAY DIFFRACTION100
2.4102-2.48120.24351350.21532682X-RAY DIFFRACTION100
2.4812-2.56120.24941540.20612637X-RAY DIFFRACTION100
2.5612-2.65280.30011160.21772696X-RAY DIFFRACTION100
2.6528-2.7590.24661230.19622707X-RAY DIFFRACTION100
2.759-2.88450.24421490.18352645X-RAY DIFFRACTION100
2.8845-3.03660.19471250.18132718X-RAY DIFFRACTION100
3.0366-3.22680.23631270.17752715X-RAY DIFFRACTION100
3.2268-3.47580.22071300.17472687X-RAY DIFFRACTION100
3.4758-3.82550.1521270.16912688X-RAY DIFFRACTION100
3.8255-4.37870.17491460.15592677X-RAY DIFFRACTION100
4.3787-5.51530.18881760.15852667X-RAY DIFFRACTION100
5.5153-46.60250.20271400.20282758X-RAY DIFFRACTION99

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