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- PDB-7zg0: Murine IL-27 in complex with IL-27Ra and a non-competing Nb -

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Basic information

Entry
Database: PDB / ID: 7zg0
TitleMurine IL-27 in complex with IL-27Ra and a non-competing Nb
Components
  • (Interleukin-27 subunit ...) x 2
  • Interleukin-27 receptor subunit alpha
  • Nanobody 5
KeywordsCYTOKINE / receptor / heterodimer / cancer / glycoprotein
Function / homology
Function and homology information


negative regulation of T cell extravasation / interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of cellular extravasation / negative regulation of T-helper 17 type immune response / Interleukin-27 signaling / Interleukin-35 Signalling / negative regulation of type 2 immune response / interleukin-27 receptor activity / regulation of isotype switching to IgG isotypes ...negative regulation of T cell extravasation / interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of cellular extravasation / negative regulation of T-helper 17 type immune response / Interleukin-27 signaling / Interleukin-35 Signalling / negative regulation of type 2 immune response / interleukin-27 receptor activity / regulation of isotype switching to IgG isotypes / response to Gram-positive bacterium / positive regulation of T-helper 1 type immune response / negative regulation of interleukin-17 production / cytokine receptor activity / negative regulation of interleukin-6 production / regulation of T cell proliferation / negative regulation of tumor necrosis factor production / T cell proliferation / positive regulation of defense response to virus by host / cytokine activity / positive regulation of type II interferon production / negative regulation of neuron apoptotic process / defense response to Gram-positive bacterium / inflammatory response / signaling receptor binding / innate immune response / cell surface / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Interleukin-27 alpha / : / IL27B N-terminal FN3 domain / : / : / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain ...Interleukin-27 alpha / : / IL27B N-terminal FN3 domain / : / : / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-27 subunit beta / Interleukin-27 receptor subunit alpha / Interleukin-27 subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsSkladanowska, K. / Bloch, Y. / Savvides, S.N.
Funding support Belgium, European Union, 5items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0E1516N Belgium
Research Foundation - Flanders (FWO)G0B4918N Belgium
Research Foundation - Flanders (FWO)12S0519N Belgium
H2020 Marie Curie Actions of the European CommissionEuropean Union
Research Foundation - Flanders (FWO)Hercules Belgium
CitationJournal: Cell Rep / Year: 2022
Title: Structural basis of activation and antagonism of receptor signaling mediated by interleukin-27.
Authors: Skladanowska, K. / Bloch, Y. / Strand, J. / White, K.F. / Hua, J. / Aldridge, D. / Welin, M. / Logan, D.T. / Soete, A. / Merceron, R. / Murphy, C. / Provost, M. / Bazan, J.F. / Hunter, C.A. ...Authors: Skladanowska, K. / Bloch, Y. / Strand, J. / White, K.F. / Hua, J. / Aldridge, D. / Welin, M. / Logan, D.T. / Soete, A. / Merceron, R. / Murphy, C. / Provost, M. / Bazan, J.F. / Hunter, C.A. / Hill, J.A. / Savvides, S.N.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-27 subunit alpha
B: Interleukin-27 subunit alpha
C: Interleukin-27 subunit beta
D: Interleukin-27 subunit beta
E: Interleukin-27 receptor subunit alpha
F: Interleukin-27 receptor subunit alpha
G: Nanobody 5
H: Nanobody 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,87014
Polymers194,1368
Non-polymers1,7346
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALLS performed.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21570 Å2
ΔGint-27 kcal/mol
Surface area58080 Å2
Unit cell
Length a, b, c (Å)167.242, 137.707, 111.479
Angle α, β, γ (deg.)90.000, 117.490, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Interleukin-27 subunit ... , 2 types, 4 molecules ABCD

#1: Protein Interleukin-27 subunit alpha / IL-27 subunit alpha / IL-27-A / IL27-A / p28


Mass: 27762.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues [1-31] belong to the non-natural signal peptide and cloning scar and are expected to be in part cotranslationally removed. Residues [238-] are part of the purification tag. Residue ...Details: Residues [1-31] belong to the non-natural signal peptide and cloning scar and are expected to be in part cotranslationally removed. Residues [238-] are part of the purification tag. Residue numbering in the pdb correspond to Uniprot sequence.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il27, Il27a / Plasmid: pHLsec / Cell line (production host): HEK293S MGat-/- / Production host: Homo sapiens (human) / References: UniProt: Q8K3I6
#2: Protein Interleukin-27 subunit beta / IL-27 subunit beta / IL-27B / Epstein-Barr virus-induced gene 3 protein homolog


Mass: 26476.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues [1-31] belong to the non-natural signal peptide and cloning scar and are expected to be in part cotranslationally removed. Residue numbering in the pdb correspond to Uniprot sequence.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ebi3, Il27b / Plasmid: pHLsec / Cell line (production host): HEK293S MGat-/- / Production host: Homo sapiens (human) / References: UniProt: O35228

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Protein / Antibody / Non-polymers , 3 types, 14 molecules EFGH

#3: Protein Interleukin-27 receptor subunit alpha / IL-27 receptor subunit alpha / IL-27R subunit alpha / IL-27R-alpha / IL-27RA / Type I T-cell ...IL-27 receptor subunit alpha / IL-27R subunit alpha / IL-27R-alpha / IL-27RA / Type I T-cell cytokine receptor / TCCR / WSX-1


Mass: 25217.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues [1-28] belong to the non-natural signal peptide and are expected to be cotranslationally removed. Residues [29-44] belong to the purification tag. Residue numbering in the pdb ...Details: Residues [1-28] belong to the non-natural signal peptide and are expected to be cotranslationally removed. Residues [29-44] belong to the purification tag. Residue numbering in the pdb correspond to Uniprot sequence.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il27ra, Tccr, Wsx1 / Plasmid: pHLsec / Cell line (production host): HEK293S MGat-/- / Production host: Homo sapiens (human) / References: UniProt: O70394
#4: Antibody Nanobody 5


Mass: 17611.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues [1-23] belong to the non-natural pelB secretion signal. Residues [24-36] belong to the purification tag which was enzymatically removed during purification.
Source: (gene. exp.) Lama glama (llama) / Plasmid: pEt15b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 6 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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.: 4 / Source method: obtained synthetically / 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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Details

Has ligand of interestN
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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Wizard screen H12 derived. 1 M Potassium sodium tartrate, 0.1 M MES/ Sodium hydroxide pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.175→100.898 Å / Num. obs: 37561 / % possible obs: 98.9 % / Redundancy: 7.028 % / Biso Wilson estimate: 76.773 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.189 / Net I/σ(I): 9.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
9.49-100.8986.7134.3914500.9990.04898
6.72-9.496.9825.1525910.9980.06699.1
5.49-6.726.8714.1633200.9910.13399.2
4.76-5.496.9514.138920.9930.1399
4.26-4.767.1411.7544440.9910.16498.8
3.89-4.267.127.2648420.9720.27399
3.6-3.897.064.153190.9150.49598.9
3.37-3.67.12.5856750.7980.79999.2
3.175-3.377.011.360290.5051.55598.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS20210323data reduction
XDS20210323data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosettafold

Resolution: 3.18→79.52 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1988 5.98 %
Rwork0.2291 31262 -
obs0.2319 33250 87.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.98 Å2 / Biso mean: 104.2347 Å2 / Biso min: 29.6 Å2
Refinement stepCycle: final / Resolution: 3.18→79.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 112 10 10646
Biso mean--151.85 44.51 -
Num. residues----1330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.18-3.260.38361580.34842437259596
3.26-3.340.37781610.302125142675100
3.34-3.440.33921580.29272480263899
3.44-3.550.32591570.27752406256395
3.55-3.680.30891510.25872366251794
3.68-3.830.30411580.25082348250692
3.83-40.28861510.23842293244490
4-4.210.29121370.22652216235387
4.21-4.480.24761340.21632115224983
4.48-4.820.25361460.18822038218481
4.82-5.310.23391320.19292008214079
5.31-6.070.25951270.21192023215079
6.07-7.650.25211100.22212029213978
7.65-79.520.23671080.19481989209776
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)
17.19671.721-3.48133.039-1.21294.9336-0.17690.1878-0.7015-0.29-0.03710.20740.3945-0.10020.2190.5649-0.1035-0.0980.6511-0.05090.77933.951913.1397-35.1642
28.0851.1944.6353.23931.41245.3109-0.19670.17450.5538-0.3506-0.0814-0.5039-0.39730.31580.26340.6025-0.12910.06110.69710.06890.768547.629836.5494-35.5956
35.5058-0.36580.44066.7633-0.07456.24790.1949-0.3047-0.871-0.3755-0.21460.40780.9448-0.54110.15260.6661-0.0406-0.11760.6350.11480.932436.46299.654-30.941
42.5146-0.4098-1.21143.31730.81183.79320.0464-1.09620.27580.56010.0875-0.0425-0.41170.3405-0.1860.8021-0.173-0.15581.3074-0.19280.76435.497132.2021-8.5556
57.0639-0.15370.03626.0529-0.89135.73920.5818-0.01840.4221-0.1185-0.4417-0.5918-0.72750.62620.00360.6516-0.08760.15450.6027-0.07220.695615.186339.8297-30.4207
62.1761-1.3262.56826.3022-3.7266.7262-0.0176-0.8428-0.330.74550.0454-0.24830.47170.2013-0.10850.8015-0.0751-0.01511.20490.1980.652316.792117.8772-8.8592
75.34982.31071.24124.71440.66286.0739-0.15870.22811.2286-2.58280.10591.3726-0.646-0.4550.15661.2313-0.2906-0.37790.8835-0.03911.780352.940765.6604-31.0769
83.5259-1.0523-1.05242.5877-1.40573.0647-0.3185-0.6580.9040.9017-0.14850.1081-0.3338-0.21680.37561.0591-0.3063-0.15961.2146-0.5911.703433.287754.5792-8.0588
90.8861-1.0248-2.21034.8083-0.41818.0415-0.15570.1072-1.3816-1.0593-0.0116-0.81490.60790.57010.18280.9946-0.16830.03220.85490.06182.084-0.9452-16.1431-30.5812
105.4559-1.06734.22353.25050.83067.68810.0957-0.4272-1.06470.83830.05120.11320.24750.4159-0.2030.8155-0.091-0.0321.14370.56371.706918.8414-5.073-7.7197
115.0196-2.88470.81923.27051.92313.4784-0.6649-0.9113-0.73071.80380.6452-0.67411.62250.60890.06411.51680.1637-0.06770.99050.33661.144148.5269-1.2281-16.1161
128.126-3.47960.88715.6829-0.65966.0605-0.1914-0.58761.00280.70220.40610.0931-1.8239-0.4075-0.18441.19480.05740.11040.73-0.12670.7183.664550.8733-15.0718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA31 - 226
2X-RAY DIFFRACTION2chain BB31 - 227
3X-RAY DIFFRACTION3chain C and (resid 33:122 or resid 230)C0
4X-RAY DIFFRACTION4chain C and resid 123:225C123 - 225
5X-RAY DIFFRACTION5chain D and (resid 33:122 or resid 226)D0
6X-RAY DIFFRACTION6chain D and (resid 123:225 or resid 230)D0
7X-RAY DIFFRACTION7chain E and (resid 32:117 or resid 224:225)E32 - 117
8X-RAY DIFFRACTION7chain E and (resid 32:117 or resid 224:225)E224 - 225
9X-RAY DIFFRACTION8chain E and resid 118:223E118 - 223
10X-RAY DIFFRACTION9chain F and (resid 32:117 or resid 224:225)F32 - 117
11X-RAY DIFFRACTION9chain F and (resid 32:117 or resid 224:225)F224 - 225
12X-RAY DIFFRACTION10chain F and resid 118:223F118 - 223
13X-RAY DIFFRACTION11chain GG-1 - 126
14X-RAY DIFFRACTION12chain HH-1 - 126

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