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- PDB-3og6: The crystal structure of human interferon lambda 1 complexed with... -

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Basic information

Entry
Database: PDB / ID: 3og6
TitleThe crystal structure of human interferon lambda 1 complexed with its high affinity receptor in space group P212121
Components
  • Interleukin 28 receptor, alpha (Interferon, lambda receptor)
  • Interleukin-29
KeywordsCYTOKINE/CYTOKINE RECEPTOR / Helical bundle / fibronectin type III domain / beta-sandwich / Cytokine signaling / 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 / innate immune response / signaling receptor binding / 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: 2.097 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: Atomic model / Data collection ...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 / 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.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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)48,7189
Polymers47,3212
Non-polymers1,3977
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint2 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.960, 85.790, 116.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 22000.043 Da / Num. of mol.: 1 / Mutation: G1A, T10P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNL1, IL29, ZCYTO21 / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q8IU54
#2: Protein Interleukin 28 receptor, alpha (Interferon, lambda receptor) / Interleukin 28 receptor / alpha (Interferon / lambda receptor) / isoform CRA_e


Mass: 25320.770 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residue 19-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_1982865, IL28RA, RP11-10N16.1-001 / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q5VTX7, UniProt: Q8IU57*PLUS

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Sugars , 2 types, 3 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 2
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 , 2 types, 270 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 20% MPEG 2000, 100 mM Tris-HCl pH 7.9, 200 mM trimethyamine N-oxide dehydrate, 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: 6.8 % / Av σ(I) over netI: 23.64 / Number: 258890 / Rmerge(I) obs: 0.07 / Χ2: 0.92 / D res high: 2.1 Å / D res low: 30 Å / Num. obs: 37819 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.523099.910.0340.9527
3.594.5210010.0461.0237.3
3.143.5910010.060.8637.4
2.853.1410010.1081.0167.4
2.652.8510010.1940.9727.4
2.492.6510010.2810.8977.4
2.372.4999.810.4160.8777.3
2.262.379910.5690.8476.6
2.182.2692.310.6920.8195.6
2.12.1879.610.840.8194.2
ReflectionResolution: 2.1→30 Å / Num. all: 38948 / Num. obs: 37819 / % possible obs: 97.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.63 Å2 / Rmerge(I) obs: 0.07 / Χ2: 0.919 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.184.20.8430440.819179.6
2.18-2.265.60.69235540.819192.3
2.26-2.376.60.56937780.847199
2.37-2.497.30.41638480.877199.8
2.49-2.657.40.28138630.8971100
2.65-2.857.40.19438710.9721100
2.85-3.147.40.10838651.0161100
3.14-3.597.40.0639180.8631100
3.59-4.527.30.04639491.0231100
4.52-3070.03441290.952199.9

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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: 2.097→29.393 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8476 / SU ML: 1.32 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1054 3.01 %Random
Rwork0.1836 ---
obs0.1849 34990 89.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.789 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 212.72 Å2 / Biso mean: 62.1478 Å2 / Biso min: 20.41 Å2
Baniso -1Baniso -2Baniso -3
1--4.4937 Å20 Å2-0 Å2
2--10.263 Å20 Å2
3----5.7693 Å2
Refinement stepCycle: LAST / Resolution: 2.097→29.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 91 266 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145713
X-RAY DIFFRACTIONf_angle_d1.22610339
X-RAY DIFFRACTIONf_chiral_restr0.123448
X-RAY DIFFRACTIONf_plane_restr0.007827
X-RAY DIFFRACTIONf_dihedral_angle_d15.0381448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0971-2.19250.36381030.29883015311865
2.1925-2.30810.34041100.23623686379680
2.3081-2.45260.22251320.1854135426788
2.4526-2.64190.20431690.15974286445593
2.6419-2.90750.2181250.16334506463196
2.9075-3.32770.20411320.16314633476598
3.3277-4.19060.18881400.15314741488199
4.1906-29.39620.21711430.184749345077100
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)
13.30740.54380.58121.51390.14191.86360.0178-0.09930.19060.0427-0.03170.0678-0.05990.11980.01820.19710.00910.01960.25040.00860.172725.119666.436961.6839
20.31420.5716-0.2672.0908-2.51833.6354-0.0478-0.1718-0.2752-0.1359-0.0024-0.30160.2979-0.0510.0180.2990.0680.01470.3220.12910.401331.417843.476177.1625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA22 - 4
2X-RAY DIFFRACTION2chain BB4 - 1

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