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- PDB-6c97: Crystal structure of FcRn at pH3 -

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Basic information

Entry
Database: PDB / ID: 6c97
TitleCrystal structure of FcRn at pH3
Components
  • Beta-2-microglobulinBeta-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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFox III, D. / Fairman, J.W.
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

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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)84,5897
Polymers84,3134
Non-polymers2763
Water8,755486
1
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4335
Polymers42,1562
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-13 kcal/mol
Surface area17050 Å2
MethodPISA
2
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)42,1562
Polymers42,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-9 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.100, 76.250, 140.150
Angle α, β, γ (deg.)90.00, 93.75, 90.00
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: 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 / 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.8 %
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.
PH range: 3.00-3.09

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59210 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.91
Reflection shellResolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 4328 / CC1/2: 0.676 / % possible all: 98.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(DEV_2443: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.616 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2
RfactorNum. reflection% reflection
Rfree0.2102 2789 4.71 %
Rwork0.1739 --
obs0.1756 59205 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5669 0 18 486 6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075984
X-RAY DIFFRACTIONf_angle_d0.8978192
X-RAY DIFFRACTIONf_dihedral_angle_d16.6813508
X-RAY DIFFRACTIONf_chiral_restr0.051851
X-RAY DIFFRACTIONf_plane_restr0.0061072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03450.33991410.24332778X-RAY DIFFRACTION99
2.0345-2.07150.31051500.24072790X-RAY DIFFRACTION98
2.0715-2.11140.26931330.22762822X-RAY DIFFRACTION99
2.1114-2.15450.25021530.2122738X-RAY DIFFRACTION99
2.1545-2.20130.28031540.20082849X-RAY DIFFRACTION99
2.2013-2.25250.27971220.20542783X-RAY DIFFRACTION98
2.2525-2.30880.23121230.20492831X-RAY DIFFRACTION99
2.3088-2.37130.25471450.20752798X-RAY DIFFRACTION99
2.3713-2.4410.25861460.20042801X-RAY DIFFRACTION99
2.441-2.51980.25791490.19872802X-RAY DIFFRACTION99
2.5198-2.60990.25971430.19572840X-RAY DIFFRACTION99
2.6099-2.71440.25141430.19422816X-RAY DIFFRACTION99
2.7144-2.83790.24291270.18482858X-RAY DIFFRACTION99
2.8379-2.98750.19221170.17832861X-RAY DIFFRACTION99
2.9875-3.17460.22241210.17072811X-RAY DIFFRACTION99
3.1746-3.41960.1831390.17242835X-RAY DIFFRACTION99
3.4196-3.76360.20461410.15162822X-RAY DIFFRACTION99
3.7636-4.30790.17941170.13582872X-RAY DIFFRACTION99
4.3079-5.42620.1471600.12452836X-RAY DIFFRACTION99
5.4262-46.6290.16641650.17622873X-RAY DIFFRACTION98
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)
11.13290.12150.07872.24590.94713.5938-0.026-0.0451-0.14250.34760.0927-0.15110.48680.37020.00220.2030.0566-0.01830.1583-0.01510.1952-6.0864-26.0064157.8261
22.8111.82251.40362.9546-0.77212.14490.0276-0.1056-0.06760.013-0.01690.2146-0.0754-0.3047-0.06830.1240.0289-0.01690.1443-0.04340.1932-15.3474-23.0131148.3621
30.71160.3833-0.46221.99581.41273.1551-0.07590.0914-0.18840.1455-0.04410.08310.5357-0.280.13870.1430.0029-0.03910.20920.00030.2554-16.0298-26.8961151.3472
41.7055-0.0425-0.14243.4023-0.54883.07430.0420.01010.2879-0.0748-0.01880.0707-0.30710.0129-0.02720.113-0.02340.00870.172-0.01140.2362-13.05439.8179160.8268
51.3377-0.6647-0.7282.70682.47325.5764-0.006-0.02350.0203-0.04420.0913-0.1215-0.0215-0.0942-0.02970.0963-0.02430.02170.17060.01690.1915-0.7112-1.5865158.1216
64.30944.35424.17164.68743.9384.50550.0403-0.0105-0.1407-0.13350.2-0.50160.26450.1571-0.47150.1371-0.00860.01060.2762-0.02250.27956.4173-7.4892150.9861
75.92765.1037-0.56737.0021-1.53075.2569-0.0774-0.1058-0.7263-0.1859-0.1099-0.84260.56360.48170.22470.20940.0484-0.01520.19480.00190.359112.1113-4.4909160.4648
84.50474.11435.01074.81376.16198.11990.1443-0.1945-0.09380.3068-0.0753-0.0290.3645-0.0916-0.09250.14220.00620.02890.1524-0.00520.2135-1.8941-10.0132155.8996
99.10682.5612-2.02037.9703-0.64759.0770.3239-0.83081.49830.362-0.14630.3842-0.8570.3433-0.1740.13660.00840.05640.3464-0.08550.45919.401210.4088165.4875
101.19971.37610.99253.86693.11626.1918-0.05240.04750.2503-0.18020.0866-0.0871-0.20360.158-0.05050.1176-0.0210.03080.20680.02080.30284.89032.018152.0793
111.2788-0.15570.33971.13570.49155.07480.0101-0.02870.14920.19110.0075-0.0802-0.3630.4476-0.01110.3435-0.05440.03490.2282-0.0630.2008-9.32257.3796192.2763
126.76090.26112.16773.73891.17977.85620.1689-0.17230.12250.3294-0.19670.33170.1256-0.82650.08560.3794-0.03870.10720.291-0.07870.2258-18.99814.461200.9034
130.25740.24060.58941.1790.13343.7618-0.006-0.21790.15630.3491-0.13960.1578-0.6457-0.66270.14140.41670.0240.08150.3638-0.08190.2623-19.76637.9903197.4998
141.8574-0.196-0.39071.8634-0.85191.28830.0974-0.1702-0.31660.18030.06960.1130.88150.0086-0.15240.7973-0.0409-0.03590.25450.02980.2231-13.9057-28.5591188.2942
153.2528-0.6223-0.83445.67725.79698.031-0.0768-0.5522-0.02980.6762-0.03620.2245-0.1026-0.21620.02790.66860.0162-0.04190.29640.01360.2329-5.5411-14.8112201.6889
162.61760.9343-0.92061.03941.77627.60830.26710.00140.12070.43840.3979-0.78780.21180.7591-0.54160.47560.097-0.03290.306-0.03550.2519-0.9909-17.4598187.8363
173.7263-3.0451-2.91446.92033.83595.95720.19330.0002-0.02230.63360.1214-0.90090.04380.3792-0.28210.4460.0242-0.14080.3913-0.05360.35213.0627-10.8379200.4159
184.174-2.7688-3.24952.14772.17052.74470.8194-0.12960.4405-0.2955-0.0493-0.692-0.43020.4623-0.68990.5835-0.019-0.02560.3841-0.1690.43353.8447-9.4528193.7853
193.1333-1.059-0.2613.26621.20633.0690.2218-0.0361-0.0740.3990.042-0.58470.36870.607-0.2010.43030.026-0.07110.3117-0.03830.29190.5276-14.6361194.3096
206.2701-1.1611-0.08892.11360.76570.29950.4274-0.5413-0.67290.62970.2633-0.23690.56510.7917-0.65720.86530.0216-0.19210.6607-0.01680.26021.9671-13.3806210.2188
217.64810.6158-0.12995.8256-0.10177.880.14950.0716-1.08690.2779-0.01020.15880.0126-0.2468-0.1120.76050.1597-0.19940.3489-0.02050.53070.1897-24.6598194.4104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 268 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 99 )
11X-RAY DIFFRACTION11chain 'C' and (resid 4 through 82 )
12X-RAY DIFFRACTION12chain 'C' and (resid 83 through 112 )
13X-RAY DIFFRACTION13chain 'C' and (resid 113 through 180 )
14X-RAY DIFFRACTION14chain 'C' and (resid 181 through 268 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 11 )
16X-RAY DIFFRACTION16chain 'D' and (resid 12 through 30 )
17X-RAY DIFFRACTION17chain 'D' and (resid 31 through 41 )
18X-RAY DIFFRACTION18chain 'D' and (resid 42 through 56 )
19X-RAY DIFFRACTION19chain 'D' and (resid 57 through 83 )
20X-RAY DIFFRACTION20chain 'D' and (resid 84 through 90 )
21X-RAY DIFFRACTION21chain 'D' and (resid 91 through 99 )

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