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Basic information

Entry
Database: PDB / ID: 3og4
TitleThe crystal structure of human interferon lambda 1 complexed with its high affinity receptor in space group P21212
Components
  • Interleukin 28 receptor, alpha (Interferon, lambda receptor)Interleukin-28 receptor
  • Interleukin-29
KeywordsCYTOKINE/CYTOKINE RECEPTOR / Helical bundle / fibronectin type III domains / beta-sandwich / Cytokine / cytokine receptor / IL-10R2 / Membrane / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


interleukin-28 receptor binding / negative regulation of memory T cell differentiation / response to type III interferon / positive regulation of MHC class I biosynthetic process / interleukin-28 receptor complex / negative regulation of type 2 immune response / negative regulation of interleukin-5 production / mucosal immune response / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...interleukin-28 receptor binding / negative regulation of memory T cell differentiation / response to type III interferon / positive regulation of MHC class I biosynthetic process / interleukin-28 receptor complex / negative regulation of type 2 immune response / negative regulation of interleukin-5 production / mucosal immune response / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / regulation of defense response to virus by host / cytokine receptor activity / Other interleukin signaling / Interleukin-20 family signaling / cell surface receptor signaling pathway via JAK-STAT / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of immune response / positive regulation of type II interferon production / defense response to virus / negative regulation of cell population proliferation / signaling receptor binding / innate immune response / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Interferon lambda / Interferon lambda / Interferon lambda superfamily / Interleukin-28A / Tissue factor / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins ...Interferon lambda / Interferon lambda / Interferon lambda superfamily / Interleukin-28A / Tissue factor / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon lambda receptor 1 / Interferon lambda-1 / Interferon lambda receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsMiknis, Z.J. / Magracheva, E. / Lei, W. / Zdanov, A. / Kotenko, S.V. / Wlodawer, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the complex of human interferon-lambda1 with its high affinity receptor interferon-lambdaR1.
Authors: Miknis, Z.J. / Magracheva, E. / Li, W. / Zdanov, A. / Kotenko, S.V. / Wlodawer, A.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Interleukin-29
B: Interleukin 28 receptor, alpha (Interferon, lambda receptor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9244
Polymers45,1172
Non-polymers8082
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint1 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.190, 65.440, 73.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Interleukin-29 / / IL-29 / Interferon lambda-1 / IFN-lambda-1 / Cytokine Zcyto21


Mass: 19795.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Purchased from Preprotech / Source: (gene. exp.) Homo sapiens (human) / Gene: IFNL1, IL29, ZCYTO21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IU54
#2: Protein Interleukin 28 receptor, alpha (Interferon, lambda receptor) / Interleukin-28 receptor / Interleukin 28 receptor / alpha (Interferon / lambda receptor) / isoform CRA_e


Mass: 25320.770 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 19-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_1982865, IL28RA, RP11-10N16.1-001 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q5VTX7, UniProt: Q8IU57*PLUS
#3: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 17% PEG 3350, 100 mM HEPES pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2009
Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 16.8 / Number: 122399 / Rmerge(I) obs: 0.057 / Χ2: 0.85 / D res high: 2.16 Å / D res low: 30 Å / Num. obs: 33364 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.653097.910.0410.833.6
3.694.6599.910.051.0073.9
3.233.6910010.0540.8523.9
2.933.2310010.0810.9693.9
2.722.9310010.1250.8643.9
2.562.7210010.1950.7753.9
2.432.5610010.2810.7523.9
2.332.4399.710.4210.7593.6
2.242.3394.110.480.9453.1
2.162.2481.710.710.6842.7
ReflectionResolution: 2.16→30 Å / Num. all: 34254 / Num. obs: 33364 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.16-2.242.70.71181.7
2.24-2.333.10.48194.1
2.33-2.433.60.421199.7
2.43-2.563.90.2811100
2.56-2.723.90.1951100
2.72-2.933.90.1251100
2.93-3.233.90.0811100
3.23-3.693.90.0541100
3.69-4.653.90.05199.9
4.65-303.60.041197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HHC and PDB entry 3G9V

3hhc

3g9v


Resolution: 2.16→29.112 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.77 / σ(F): 0.1 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 926 2.99 %
Rwork0.1977 --
obs0.1989 31018 90.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.289 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.2817 Å2-0 Å2-0 Å2
2---7.2619 Å20 Å2
3----4.2502 Å2
Refinement stepCycle: LAST / Resolution: 2.16→29.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 53 150 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052819
X-RAY DIFFRACTIONf_angle_d1.0573835
X-RAY DIFFRACTIONf_dihedral_angle_d16.3661052
X-RAY DIFFRACTIONf_chiral_restr0.068436
X-RAY DIFFRACTIONf_plane_restr0.004481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.27380.39411030.33763167X-RAY DIFFRACTION68
2.2738-2.41620.311030.25593735X-RAY DIFFRACTION80
2.4162-2.60270.26681260.22544352X-RAY DIFFRACTION92
2.6027-2.86440.28851580.21534529X-RAY DIFFRACTION96
2.8644-3.27840.25331410.20144663X-RAY DIFFRACTION99
3.2784-4.12860.23191460.1724754X-RAY DIFFRACTION99
4.1286-29.11450.20831490.18564892X-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)
13.5223-0.2194-0.60763.3470.55213.50430.07830.23460.0178-0.3091-0.04460.083-0.0990.0132-0.00010.4937-0.04410.00220.3688-0.02520.379328.161823.355-0.3236
23.76850.6512-0.81561.6192-0.17081.9564-0.1824-0.3454-0.0476-0.00920.2277-0.0909-0.1632-0.056600.40530.0753-0.04010.4310.02960.384322.809234.070625.4922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B

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