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- PDB-8q3j: Crystal structure of mIL-38 in complex with a neutralizing Fab e0... -

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Basic information

Entry
Database: PDB / ID: 8q3j
TitleCrystal structure of mIL-38 in complex with a neutralizing Fab e04 fragment
Components
  • Fab e04 Heavy Chain (e04 HC)
  • Fab e04 Light Chain (e04 LC)
  • Interleukin-1 family member 10
KeywordsCYTOKINE / IL-38 / Fab / anti-tumor Immunity / Neutralizing antibody / Chemotherapy
Function / homology
Function and homology information


Interleukin-38 signaling / Interleukin-36 pathway / inflammatory response to antigenic stimulus / interleukin-1 receptor binding / endoplasmic reticulum-Golgi intermediate compartment / cytokine activity / cytokine-mediated signaling pathway / cellular response to lipopolysaccharide / positive regulation of gene expression / extracellular space
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF
Similarity search - Domain/homology
PHOSPHATE ION / Interleukin-1 family member 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGarcia-Pardo, J. / Da Silva, P. / Mora, J. / Wiechmann, S. / Putyrski, M. / You, X. / Kannt, A. / Ernst, A. / Brune, B. / Weigert, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other governmentFraunhofer Institute for Molecular Biology and Applied Ecology IME Germany
CitationJournal: J Immunother Cancer / Year: 2024
Title: Neutralizing IL-38 activates gamma delta T cell-dependent antitumor immunity and sensitizes for chemotherapy.
Authors: da Silva, P. / Mora, J. / You, X. / Wiechmann, S. / Putyrski, M. / Garcia-Pardo, J. / Kannt, A. / Ernst, A. / Bruene, B. / Weigert, A.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 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-1 family member 10
B: Fab e04 Light Chain (e04 LC)
C: Fab e04 Heavy Chain (e04 HC)
D: Interleukin-1 family member 10
E: Fab e04 Light Chain (e04 LC)
F: Fab e04 Heavy Chain (e04 HC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,07510
Polymers134,6956
Non-polymers3804
Water1,964109
1
A: Interleukin-1 family member 10
B: Fab e04 Light Chain (e04 LC)
C: Fab e04 Heavy Chain (e04 HC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5375
Polymers67,3473
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-44 kcal/mol
Surface area25090 Å2
MethodPISA
2
D: Interleukin-1 family member 10
E: Fab e04 Light Chain (e04 LC)
F: Fab e04 Heavy Chain (e04 HC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5375
Polymers67,3473
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-40 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.800, 66.940, 129.050
Angle α, β, γ (deg.)90.000, 104.727, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Interleukin-1 family member 10


Mass: 17095.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il1f10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8R459
#2: Antibody Fab e04 Light Chain (e04 LC)


Mass: 24599.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F cells / Production host: Homo sapiens (human)
#3: Antibody Fab e04 Heavy Chain (e04 HC)


Mass: 25652.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293F cells / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 27.5% (w/v) PEG 1500 100 mM SPG buffer, pH 8.7

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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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→70.11 Å / Num. obs: 50677 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 55.59 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.41
Reflection shellResolution: 2.35→2.49 Å / Num. unique obs: 8129 / CC1/2: 0.99 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19.2_4158refinement
MxCuBEdata collection
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→70.11 Å / SU ML: 0.3854 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.3593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2826 4207 10 %
Rwork0.2272 37877 -
obs0.2328 42084 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→70.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8793 0 20 109 8922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00879019
X-RAY DIFFRACTIONf_angle_d1.108412242
X-RAY DIFFRACTIONf_chiral_restr0.05541357
X-RAY DIFFRACTIONf_plane_restr0.01021556
X-RAY DIFFRACTIONf_dihedral_angle_d16.70263252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.38051370.32281235X-RAY DIFFRACTION98.56
2.53-2.560.37781410.33061267X-RAY DIFFRACTION99.44
2.56-2.590.42791390.32211243X-RAY DIFFRACTION99.21
2.59-2.620.35271410.29951262X-RAY DIFFRACTION98.94
2.62-2.660.40851380.29241244X-RAY DIFFRACTION99.42
2.66-2.690.3731440.27781292X-RAY DIFFRACTION99.17
2.69-2.730.32991360.27351228X-RAY DIFFRACTION99.42
2.73-2.770.3531390.27211251X-RAY DIFFRACTION99.14
2.77-2.820.31391380.2581246X-RAY DIFFRACTION99.21
2.82-2.860.34331420.25991273X-RAY DIFFRACTION99.51
2.86-2.910.37081410.24891266X-RAY DIFFRACTION99.29
2.91-2.960.31661380.26711241X-RAY DIFFRACTION99.21
2.96-3.020.34221420.26871278X-RAY DIFFRACTION99.3
3.02-3.080.33981370.26921234X-RAY DIFFRACTION99.13
3.08-3.150.37351390.26941261X-RAY DIFFRACTION98.87
3.15-3.220.36651410.29381268X-RAY DIFFRACTION98.67
3.22-3.30.32511390.26181246X-RAY DIFFRACTION98.58
3.3-3.390.35471360.24481240X-RAY DIFFRACTION98.71
3.39-3.490.26231400.2191259X-RAY DIFFRACTION98.45
3.49-3.610.27741380.21731247X-RAY DIFFRACTION98.44
3.61-3.730.28861410.23991267X-RAY DIFFRACTION98.53
3.73-3.880.28171410.24681264X-RAY DIFFRACTION99.57
3.88-4.060.28911390.22571259X-RAY DIFFRACTION99.79
4.06-4.270.22361400.19121284X-RAY DIFFRACTION99.44
4.27-4.540.25031440.18181285X-RAY DIFFRACTION99.58
4.54-4.890.19081410.17381273X-RAY DIFFRACTION99.51
4.89-5.390.25661420.18471275X-RAY DIFFRACTION99.37
5.39-6.160.27121440.21171296X-RAY DIFFRACTION99.31
6.17-7.760.24621420.22881274X-RAY DIFFRACTION98.4
7.77-70.110.24231470.2041319X-RAY DIFFRACTION98.13

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