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- PDB-7ox4: Mouse interleukin-9 in complex with Fab 35D8. -

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Basic information

Entry
Database: PDB / ID: 7ox4
TitleMouse interleukin-9 in complex with Fab 35D8.
Components
  • Heavy chain (Fab 35D8)
  • Interleukin-9
  • Light chain (Fab 35D8)
KeywordsCYTOKINE / IL-9 / Fab
Function / homology
Function and homology information


Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / cytokine receptor binding / regulation of receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / B cell proliferation / B cell differentiation / cytokine activity / growth factor activity / extracellular space
Similarity search - Function
Interleukin-9 / Interleukin-7/Interleukin-9, conserved site / Interleukin-7 and -9 signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Interleukin-9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDe Vos, T. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S56318N Belgium
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9)
Authors: De Vos, T. / Godar, M. / Bick, F. / Papageorgiou, A.C. / Evangelidis, T. / Markovic, I. / Mortier, E. / Dumoutier, L. / Tripsianes, K. / Blanchetot, C. / Savvides, S.N.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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: Heavy chain (Fab 35D8)
B: Light chain (Fab 35D8)
C: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,09217
Polymers61,1953
Non-polymers89714
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-348 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.210, 78.920, 192.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Interleukin-9 / IL-9 / Cytokine P40 / T-cell growth factor P40


Mass: 14597.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15247

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Antibody , 2 types, 2 molecules AB

#1: Antibody Heavy chain (Fab 35D8)


Mass: 24150.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain (Fab 35D8)


Mass: 22446.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 330 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Zinc acetate, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→48.02 Å / Num. obs: 49669 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.997 / Net I/σ(I): 9.49
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 7855 / CC1/2: 0.443

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZS7, 5BV7

4zs7

5bv7


Resolution: 1.8→48.02 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2482 5 %
Rwork0.1834 47165 -
obs0.1857 49647 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.15 Å2 / Biso mean: 40.6289 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 1.8→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 23 316 4426
Biso mean--58.75 42.41 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.37081300.34062499262997
1.84-1.870.34411380.292926192757100
1.87-1.910.29351360.264125682704100
1.91-1.960.27481380.238826332771100
1.96-2.010.3141350.237625692704100
2.01-2.060.30981370.236525952732100
2.06-2.120.27111380.225826252763100
2.12-2.190.25611370.216225942731100
2.19-2.270.26051370.20226002737100
2.27-2.360.25621360.19425902726100
2.36-2.470.20581380.18626312769100
2.47-2.60.26271380.182126212759100
2.6-2.760.21461390.186726252764100
2.76-2.970.21811380.176626322770100
2.97-3.270.22521400.176826542794100
3.27-3.740.20871390.162426502789100
3.74-4.720.17951410.144126692810100
4.72-48.020.21031470.165227912938100
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)
11.17930.24020.88570.38770.95464.87570.0463-0.33070.10980.2187-0.18860.16770.1334-0.45930.06560.2615-0.03680.07630.2311-0.05120.2286-25.5868-2.205225.9129
23.1275-2.64740.40065.5144-0.01080.7277-0.02420.0906-0.01030.0691-0.0695-0.14690.10930.10840.08420.13710.01650.01630.15460.00540.1603-13.9194-22.28614.0849
33.3939-1.041-2.15582.03541.93545.17030.1606-0.3150.18860.2962-0.0472-0.1895-0.01150.2282-0.11160.2315-0.0315-0.01280.2639-0.02040.1995-3.57321.462128.7723
45.17851.61251.50562.30591.29863.13530.1131-0.34950.23090.1208-0.08820.0761-0.006-0.211-0.01240.14620.03070.00590.1749-0.00130.2278-4.5939-13.4769-2.1243
57.03532.0242.29463.89871.54853.6359-0.06270.52140.0899-0.22650.13990.0002-0.07890.0318-0.04020.1754-0.00160.00960.1830.03920.1859-2.7404-15.0642-10.2812
64.0913-1.97450.54715.9088-2.88132.1072-0.12910.2997-0.0350.1701-0.008-0.0224-0.398-0.70390.17370.41750.00020.03530.3752-0.06780.2315-25.38956.574347.8084
78.11211.02850.53425.9860.2227.36710.048-1.1610.4591.4744-0.48140.18720.14340.34960.61920.691-0.08760.02510.6347-0.04130.4176-25.22583.478168.4418
83.6002-0.1264-0.73595.76921.41065.61350.0406-0.48970.32680.40270.0909-0.3004-0.70850.5239-0.16250.4406-0.08870.00360.419-0.08220.2764-18.34311.763955.1438
91.7815-0.43151.04694.48192.08922.29290.3828-0.42070.8683-0.1064-0.00240.6882-0.98120.3926-0.34210.9781-0.02390.1290.6305-0.1560.5285-23.014222.601957.0163
104.99350.9868-0.6673.7707-3.87794.01640.22880.33160.61410.07440.27980.7416-0.852-0.6381-0.44140.61480.08330.05440.4896-0.06920.4243-28.497514.640651.3179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )A1 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 224 )A130 - 224
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 115 )B2 - 115
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 175 )B116 - 175
5X-RAY DIFFRACTION5chain 'B' and (resid 176 through 211 )B176 - 211
6X-RAY DIFFRACTION6chain 'C' and (resid 21 through 37 )C21 - 37
7X-RAY DIFFRACTION7chain 'C' and (resid 38 through 56 )C38 - 56
8X-RAY DIFFRACTION8chain 'C' and (resid 57 through 101 )C57 - 101
9X-RAY DIFFRACTION9chain 'C' and (resid 102 through 120 )C102 - 120
10X-RAY DIFFRACTION10chain 'C' and (resid 121 through 139 )C121 - 139

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