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- PDB-6c98: Crystal structure of FcRn bound to UCB-84 -

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Basic information

Entry
Database: PDB / ID: 6c98
TitleCrystal structure of FcRn bound to UCB-84
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 / positive regulation of receptor binding / early endosome lumen / 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 / positive regulation of receptor binding / early endosome lumen / 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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / 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
CYSTEINE / Chem-ER7 / DI(HYDROXYETHYL)ETHER / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFox III, D. / Lukacs, C.M.
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)85,38611
Polymers84,3134
Non-polymers1,0737
Water8,071448
1
A: IgG receptor FcRn large subunit p51
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7466
Polymers42,1562
Non-polymers5904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-9 kcal/mol
Surface area16670 Å2
MethodPISA
2
C: IgG receptor FcRn large subunit p51
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6405
Polymers42,1562
Non-polymers4843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-11 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.270, 76.290, 138.060
Angle α, β, γ (deg.)90.00, 90.01, 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 / 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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Non-polymers , 5 types, 455 molecules

#3: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-ER7 / 1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one


Mass: 270.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11FN4O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
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 3.0 AND 20% 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 PEG 6,000, AND 20% GLYCEROL AND 20MM UCB-84).
PH range: 3.0-3.09

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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: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 73773 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.52
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 5452 / CC1/2: 0.669 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(DEV_2443: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.421 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.63
RfactorNum. reflection% reflection
Rfree0.2134 3693 5.01 %
Rwork0.1723 --
obs0.1744 73740 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→40.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 71 448 6099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075986
X-RAY DIFFRACTIONf_angle_d0.9488214
X-RAY DIFFRACTIONf_dihedral_angle_d16.2353547
X-RAY DIFFRACTIONf_chiral_restr0.056865
X-RAY DIFFRACTIONf_plane_restr0.0061074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87430.28361440.2282663X-RAY DIFFRACTION98
1.8743-1.90.30741710.25032646X-RAY DIFFRACTION98
1.9-1.92720.43091280.30922645X-RAY DIFFRACTION95
1.9272-1.95590.28371550.22342549X-RAY DIFFRACTION98
1.9559-1.98650.2341520.18862722X-RAY DIFFRACTION99
1.9865-2.01910.18841360.17892720X-RAY DIFFRACTION99
2.0191-2.05390.25591300.17662643X-RAY DIFFRACTION98
2.0539-2.09120.27211430.22062639X-RAY DIFFRACTION96
2.0912-2.13140.27751320.17142719X-RAY DIFFRACTION99
2.1314-2.17490.16981330.16692677X-RAY DIFFRACTION99
2.1749-2.22220.21851270.16332733X-RAY DIFFRACTION99
2.2222-2.27390.28141410.21742577X-RAY DIFFRACTION96
2.2739-2.33080.22151160.17642762X-RAY DIFFRACTION99
2.3308-2.39380.22541450.17162692X-RAY DIFFRACTION99
2.3938-2.46420.20841430.16342720X-RAY DIFFRACTION99
2.4642-2.54380.27021260.17172715X-RAY DIFFRACTION99
2.5438-2.63470.221330.18262758X-RAY DIFFRACTION99
2.6347-2.74010.22531590.17792624X-RAY DIFFRACTION98
2.7401-2.86480.20591390.16952704X-RAY DIFFRACTION99
2.8648-3.01580.18711550.16462741X-RAY DIFFRACTION99
3.0158-3.20470.20981250.16912715X-RAY DIFFRACTION99
3.2047-3.4520.18751390.16782728X-RAY DIFFRACTION99
3.452-3.79910.181610.15422719X-RAY DIFFRACTION99
3.7991-4.34830.19411560.14032698X-RAY DIFFRACTION99
4.3483-5.47630.19331730.13582735X-RAY DIFFRACTION99
5.4763-40.43040.18531310.19092803X-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)
11.58790.0744-0.21881.8411-0.76983.6402-0.05820.00870.14590.17590.0182-0.0388-0.46340.07620.02320.1680.00250.00110.10110.03440.148122.173326.19411.3536
20.421-0.0575-0.21712.0509-0.57911.94730.01030.0438-0.03220.48790.0005-0.08070.04160.01410.00940.06040.0211-0.01410.1907-0.00990.171325.01063.017523.7753
31.66380.4141-0.04912.67720.10212.40310.02430.0195-0.1988-0.02210.0202-0.30220.25530.0669-0.03280.1230.00410.00060.1463-0.00270.163827.0262-8.503421.4997
41.0119-0.1322-0.12364.0421-3.52433.19480.0590.1645-0.1038-0.40660.02990.04910.37980.3150.04660.1689-0.04030.00020.204-0.00410.150814.42132.86369.3143
54.55071.6674-1.64880.6846-0.70722.0940.1017-0.5176-0.23030.32350.14160.3912-0.02290.0329-0.12850.2057-0.00840.03130.26390.08610.220811.9799-5.408531.024
60.87790.2478-0.99211.7891-1.83293.7818-0.03380.04730.1415-0.0010.20.25480.0534-0.2976-0.12750.1176-0.0188-0.00190.18540.02690.163511.86123.056619.2977
70.35890.0404-0.13240.37090.38660.95680.093-0.16180.1691-0.0885-0.01680.3895-0.1421-0.04490.08250.1474-0.0019-0.00910.2190.06310.2325.64856.899211.2632
81.57211.9217-0.26762.3116-0.52290.46240.02-0.2304-0.003-0.0852-0.10310.3079-0.0126-0.05510.07160.14110.02510.01570.20050.04890.24819.2748.811616.1076
92.09111.7146-2.21683.6211-3.18713.6557-0.00550.06350.1336-0.00480.33440.44670.1234-0.517-0.33220.1093-0.01140.00770.17880.04320.19649.94626.082920.464
100.80780.5905-0.66021.7886-2.02873.5451-0.0860.0785-0.054-0.33450.24810.30440.3135-0.4659-0.1280.1938-0.0514-0.05590.28950.04780.27143.995-1.80812.7526
113.4808-0.80570.8244.0228-1.79854.82140.0959-0.0362-0.7424-0.1447-0.1639-0.33220.45350.75620.03030.2161-0.033-0.00130.22130.03730.380910.2161-7.688718.1702
121.1763-0.14460.42821.8794-0.51322.9702-0.08750.1245-0.1375-0.33950.07210.06690.475-0.18320.01540.2131-0.0394-0.02030.15010.02650.154817.6959-13.250751.1418
132.5927-1.17860.11681.95780.43862.482-0.05720.06170.2749-0.03430.1098-0.281-0.02030.3587-0.10690.1367-0.0088-0.01150.19780.05310.172827.6958-10.778660.5219
140.729-0.1336-0.22821.3013-0.49712.0123-0.0665-0.1004-0.1889-0.1404-0.0631-0.12990.55430.26660.1050.23070.02980.00680.18770.02420.23327.4973-14.868258.0279
151.7389-0.20930.25522.54850.242.66690.0036-0.03720.2696-0.01760.0147-0.1806-0.3498-0.0237-0.01750.14120.0038-0.0030.1512-0.00920.165625.191121.591148.0736
160.77230.27990.5012.846-4.08859.31930.0176-0.13420.1110.2570.11890.0193-0.18640.2387-0.0840.17340.06410.01050.1909-0.00020.158314.41278.667259.6893
175.2751-3.24491.84552.2985-1.75011.96290.30210.53940.2527-0.27830.13740.2844-0.051-0.226-0.22510.20410.023-0.03790.2950.09570.242611.896516.875837.6691
180.7783-0.21260.89991.5634-1.82973.668-0.09660.0048-0.14170.03130.23180.2409-0.1291-0.366-0.11710.13340.0251-0.00240.19320.03370.169111.86168.488649.7254
193.6201-3.87483.89324.9913-4.67115.21340.06820.0108-0.2480.00820.10440.40.1762-0.1488-0.12950.15740.01420.01740.21230.05170.2325.79744.789557.5618
202.6611-2.65170.47622.7606-0.30950.09490.11750.1683-0.3425-0.0118-0.11490.580.0265-0.112-0.01910.1546-0.0256-0.01970.24550.02370.2935.3913.77550.0332
210.8389-0.32730.121.5976-0.92811.5184-0.0327-0.02260.07910.21230.14270.2249-0.1633-0.3347-0.08530.12930.01680.01840.20190.03140.19488.64628.581754.4255
223.34140.684-0.80273.7474-1.76865.13380.0283-0.00270.60010.2129-0.1053-0.2396-0.29290.7152-0.06470.2090.0364-0.00090.22940.03630.348810.20319.263450.8774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:157 )A4 - 157
2X-RAY DIFFRACTION2( CHAIN A AND RESID 158:201 )A158 - 201
3X-RAY DIFFRACTION3( CHAIN A AND RESID 202:267 )A202 - 267
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:11 )B1 - 11
5X-RAY DIFFRACTION5( CHAIN B AND RESID 12:19 )B12 - 19
6X-RAY DIFFRACTION6( CHAIN B AND RESID 20:30 )B20 - 30
7X-RAY DIFFRACTION7( CHAIN B AND RESID 31:41 )B31 - 41
8X-RAY DIFFRACTION8( CHAIN B AND RESID 42:61 )B42 - 61
9X-RAY DIFFRACTION9( CHAIN B AND RESID 62:71 )B62 - 71
10X-RAY DIFFRACTION10( CHAIN B AND RESID 72:90 )B72 - 90
11X-RAY DIFFRACTION11( CHAIN B AND RESID 91:99 )B91 - 99
12X-RAY DIFFRACTION12( CHAIN C AND RESID 4:81 )C4 - 81
13X-RAY DIFFRACTION13( CHAIN C AND RESID 82:112 )C82 - 112
14X-RAY DIFFRACTION14( CHAIN C AND RESID 113:180 )C113 - 180
15X-RAY DIFFRACTION15( CHAIN C AND RESID 181:267 )C181 - 267
16X-RAY DIFFRACTION16( CHAIN D AND RESID 1:11 )D1 - 11
17X-RAY DIFFRACTION17( CHAIN D AND RESID 12:19 )D12 - 19
18X-RAY DIFFRACTION18( CHAIN D AND RESID 20:30 )D20 - 30
19X-RAY DIFFRACTION19( CHAIN D AND RESID 31:41 )D31 - 41
20X-RAY DIFFRACTION20( CHAIN D AND RESID 42:56 )D42 - 56
21X-RAY DIFFRACTION21( CHAIN D AND RESID 57:90 )D57 - 90
22X-RAY DIFFRACTION22( CHAIN D AND RESID 91:99 )D91 - 99

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