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- PDB-5t5w: Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbe... -

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Basic information

Entry
Database: PDB / ID: 5t5w
TitleStructure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex
Components
  • Interferon lambda receptor 1
  • Interferon lambda-3
  • Interleukin-10 receptor subunit beta
KeywordsCYTOKINE/CYTOKINE RECEPTOR / receptor / cytokine / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


interleukin-10 receptor activity / response to type III interferon / interleukin-28 receptor complex / mucosal immune response / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / interleukin-10-mediated signaling pathway / regulation of defense response to virus by host / cytokine receptor activity / Other interleukin signaling ...interleukin-10 receptor activity / response to type III interferon / interleukin-28 receptor complex / mucosal immune response / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / interleukin-10-mediated signaling pathway / regulation of defense response to virus by host / cytokine receptor activity / Other interleukin signaling / Interleukin-20 family signaling / negative regulation of viral genome replication / Interleukin-10 signaling / cell surface receptor signaling pathway via JAK-STAT / coreceptor activity / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of immune response / cellular response to virus / cytokine-mediated signaling pathway / signaling receptor activity / defense response to virus / immune response / inflammatory response / signaling receptor binding / negative regulation of cell population proliferation / innate immune response / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Interferon lambda / Interferon lambda superfamily / Interleukin-28A / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Interferon lambda / Interferon lambda superfamily / Interleukin-28A / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-10 receptor subunit beta / Interferon lambda receptor 1 / Interferon lambda-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.847 Å
AuthorsMendoza, J.L. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI109662 United States
CitationJournal: Immunity / Year: 2017
Title: The IFN-lambda-IFN-lambda R1-IL-10R beta Complex Reveals Structural Features Underlying Type III IFN Functional Plasticity.
Authors: Mendoza, J.L. / Schneider, W.M. / Hoffmann, H.H. / Vercauteren, K. / Jude, K.M. / Xiong, A. / Moraga, I. / Horton, T.M. / Glenn, J.S. / de Jong, Y.P. / Rice, C.M. / Garcia, K.C.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 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 1.7Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.8Oct 4, 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
Revision 1.9Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-10 receptor subunit beta
B: Interferon lambda receptor 1
C: Interferon lambda-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3256
Polymers69,6613
Non-polymers6643
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-9 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.790, 106.790, 129.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Interleukin-10 receptor subunit beta / IL-10RB / Cytokine receptor class-II member 4 / Cytokine receptor family 2 member 4 / CRF2-4 / ...IL-10RB / Cytokine receptor class-II member 4 / Cytokine receptor family 2 member 4 / CRF2-4 / Interleukin-10 receptor subunit 2 / IL-10R2


Mass: 25045.900 Da / Num. of mol.: 1 / Fragment: UNP residues 20-220 / Mutation: N49Q, N68Q, N102Q, N161Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL10RB, CRFB4, D21S58, D21S66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08334
#2: Protein Interferon lambda receptor 1 / IFN-lambda-R1 / Cytokine receptor class-II member 12 / Cytokine receptor family 2 member 12 / CRF2- ...IFN-lambda-R1 / Cytokine receptor class-II member 12 / Cytokine receptor family 2 member 12 / CRF2-12 / Interleukin-28 receptor subunit alpha / IL-28RA / Likely interleukin or cytokine receptor 2 / LICR2


Mass: 24703.340 Da / Num. of mol.: 1 / Fragment: UNP residues 21-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNLR1, IL28RA, LICR2 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q8IU57
#3: Protein Interferon lambda-3 / IFN-lambda-3 / Cytokine Zcyto22 / Interleukin-28B / IL-28B / Interleukin-28C / IL-28C


Mass: 19911.914 Da / Num. of mol.: 1 / Fragment: UNP residues 34-195 / Mutation: Q15R, E73D, H120R, T150A, V163E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNL3, IL28B, IL28C, ZCYTO22 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IZI9
#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.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: .2 M Ca acetate, .1 M Imidazole pH 8.0, 10% PEG8000, 3% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2016
RadiationMonochromator: multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999975 Å / Relative weight: 1
ReflectionResolution: 2.847→46.241 Å / Num. obs: 20507 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 21 % / Biso Wilson estimate: 106.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
2.85-2.92213.2431.130.47799.8
2.92-32.2351.730.699100
3-3.091.6522.420.769100
3.09-3.181.0134.090.901100
3.18-3.290.7485.570.943100
3.29-3.40.4938.210.976100
3.4-3.530.34511.390.986100
3.53-3.680.21617.320.994100
3.68-3.840.15922.010.997100
3.84-4.030.11328.660.99899.9
4.03-4.240.09135.80.998100
4.24-4.50.07342.510.999100
4.5-4.810.0648.480.999100
4.81-5.20.05652.160.999100
5.2-5.690.05652.420.999100
5.69-6.370.05652.370.999100
6.37-7.350.04955.861100
7.35-90.04261.571100
9-12.730.03763.411100
12.730.0459.540.99994.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSOct 15, 2015data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OG6, 3LQM

3og6

3lqm


Resolution: 2.847→46.241 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1036 5.05 %random selection
Rwork0.1981 ---
obs0.2009 20499 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.847→46.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 42 18 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054374
X-RAY DIFFRACTIONf_angle_d0.6945990
X-RAY DIFFRACTIONf_dihedral_angle_d9.3122620
X-RAY DIFFRACTIONf_chiral_restr0.045683
X-RAY DIFFRACTIONf_plane_restr0.005765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8473-2.99740.53241400.43292721X-RAY DIFFRACTION100
2.9974-3.18510.36861480.30732746X-RAY DIFFRACTION100
3.1851-3.4310.35431480.26552760X-RAY DIFFRACTION100
3.431-3.77610.3161490.232742X-RAY DIFFRACTION100
3.7761-4.32210.23831440.1822787X-RAY DIFFRACTION100
4.3221-5.44410.19491480.16032801X-RAY DIFFRACTION100
5.4441-46.24750.23151590.18062906X-RAY DIFFRACTION100
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)
16.63115.9639-2.52044.3267-2.62380.77770.2008-1.1337-2.5907-0.23640.2795-1.27071.8562-0.2957-0.11481.6236-0.3724-0.32040.92910.43961.412873.414660.4996167.1059
28.3546.7476-1.2895.2618-0.39879.2366-0.15941.09680.5004-1.50090.65020.26921.57-0.9802-0.47341.1187-0.1156-0.32760.73280.17551.219870.582465.873157.8345
38.54162.83062.35732.44730.20284.00160.5493-0.5576-0.9326-0.4525-0.0377-0.06120.8765-0.0171-0.50020.86760.1633-0.12340.58180.05430.754685.482973.4144164.4479
43.44760.51052.95774.01861.09396.8215-0.1863-1.0230.31870.3581-0.2066-0.546-0.37480.13620.12690.71930.2288-0.02641.02020.06410.7185100.914780.7106176.0031
58.9999-1.2515-0.72239.5072-1.83727.8952-0.5113-0.995-1.34680.45780.2616-0.51510.27571.23810.20890.68810.2787-0.15781.142-0.02970.5859103.829278.5126177.0171
68.2272-6.06796.01537.4035-0.76138.7085-0.2111.3881-1.5728-0.5881-0.3962-1.454-0.36432.6320.64470.78570.1831-0.25462.073-0.05991.7983119.194775.0206176.9211
70.1862.7614-1.44267.9832-6.24144.6829-0.57321.039-0.1782-2.11220.4004-0.4592-1.44582.57510.08581.85540.24440.27171.31930.1611.009696.44494.4593130.2049
82.16717.0339-0.78326.487-0.77040.1094-1.7256-0.2428-1.19920.81480.7589-3.3555-0.39-0.40382.8452.58530.52050.18591.59690.84240.995192.8075101.2027123.6595
94.63062.1618-2.90783.4003-0.20473.4171.3326-0.1797-1.2386-1.3998-1.0692-0.75250.59930.0121-1.46842.71130.37870.15351.21650.31431.035681.4215102.4001129.8419
100.7257-1.01942.40581.6247-2.99995.9685-0.12550.57650.6184-1.86370.1558-0.12460.1568-0.4663-0.15092.4430.20110.21861.230.18550.849590.246399.7883128.7953
114.5242-5.33373.99966.1403-2.376.4897-0.44160.26620.7078-0.2158-0.0698-1.4922-0.74530.87250.46390.87830.02870.28211.07710.03421.1493105.4693.8209153.0386
123.33273.03241.24173.11711.02550.12660.26842.1946-1.1931-1.0418-0.4317-1.08021.1850.7819-0.00531.11640.37430.34041.4528-0.14120.9637111.504781.6386153.4603
134.0102-1.79110.79020.6276-0.34830.6216-0.45340.12930.4362-0.45060.3156-1.27690.02270.94130.06431.02050.120.3181.3065-0.02661.3268110.599486.1636154.0929
144.6908-4.36471.25724.214-3.4876.24850.46170.9436-0.6677-0.8640.1785-0.02281.66671.2536-0.57391.0499-0.0215-0.28290.9787-0.02750.830979.242386.7898149.322
152.091-2.6126-3.74316.17746.09226.81630.2760.96510.0116-0.963-0.52582.0705-0.14490.26250.98142.0115-0.1863-0.2711.07970.02751.481871.7769102.9841142.4174
166.8569-3.22673.94777.13122.09896.57820.54520.75450.5956-0.5053-0.51731.23730.2802-0.17150.03890.87250.122-0.22530.70540.00510.745672.74298.9107154.5597
1710.0041-2.929-2.74825.4615-0.56647.30140.1270.32630.1381-0.8334-0.22362.5654-0.318-0.91790.10510.7588-0.067-0.47830.7561-0.02911.099769.560295.7186153.8349
186.1082-2.30353.96522.28732.30197.5645-0.30330.02930.9709-1.5065-0.33950.5902-1.92030.20670.63061.256-0.0095-0.23330.58620.10570.661378.757697.4937150.2319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 217 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 22 )
8X-RAY DIFFRACTION8chain 'B' and (resid 23 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 102 )
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 135 )
12X-RAY DIFFRACTION12chain 'B' and (resid 136 through 154 )
13X-RAY DIFFRACTION13chain 'B' and (resid 155 through 201 )
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 33 )
15X-RAY DIFFRACTION15chain 'C' and (resid 34 through 48 )
16X-RAY DIFFRACTION16chain 'C' and (resid 49 through 78 )
17X-RAY DIFFRACTION17chain 'C' and (resid 79 through 133 )
18X-RAY DIFFRACTION18chain 'C' and (resid 134 through 163 )

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