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- PDB-7ox3: Fab 6D3: hIL-9 complex -

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Basic information

Entry
Database: PDB / ID: 7ox3
TitleFab 6D3: hIL-9 complex
Components
  • Heavy chain (Fab 6D3)
  • Interleukin-9
  • Light chain (Fab 6D3)
KeywordsCYTOKINE / IL-9 / complex
Function / homology
Function and homology information


interleukin-9 receptor binding / Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / B cell proliferation / B cell differentiation / cytokine activity / growth factor activity ...interleukin-9 receptor binding / Interleukin-9 signaling / interleukin-9-mediated signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / immunoglobulin mediated immune response / B cell proliferation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of cell growth / inflammatory response / positive regulation of cell population proliferation / extracellular space / extracellular region
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
B: Light chain (Fab 6D3)
A: Heavy chain (Fab 6D3)
C: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4408
Polymers60,9593
Non-polymers4805
Water7,638424
1
B: Light chain (Fab 6D3)
A: Heavy chain (Fab 6D3)
hetero molecules

C: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4408
Polymers60,9593
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area5260 Å2
ΔGint-104 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.480, 81.860, 116.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-546-

HOH

21B-556-

HOH

31C-371-

HOH

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Components

#1: Antibody Light chain (Fab 6D3)


Mass: 22661.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Heavy chain (Fab 6D3)


Mass: 23746.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Interleukin-9 / IL-9 / Cytokine P40 / T-cell growth factor P40


Mass: 14551.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15248
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M ammonium sulfate, 0.1M Tris, 16% PEG 1500, pH 5.8

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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 EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→48.64 Å / Num. obs: 63819 / % possible obs: 99.2 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 21.59
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 10037 / CC1/2: 0.703

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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: 5NIV, 6CT7

5niv

6ct7


Resolution: 1.7→48.64 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 3188 5 %
Rwork0.1764 60614 -
obs0.1781 63802 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108 Å2 / Biso mean: 40.291 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 1.7→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 25 424 4546
Biso mean--71.13 45.12 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.730.38581290.33582479260895
1.73-1.750.29851380.28832611274999
1.75-1.780.31811360.25842585272198
1.78-1.810.26221350.247325762711100
1.81-1.850.29331380.23932610274899
1.85-1.880.25671380.2226162754100
1.88-1.920.27951360.222596273299
1.92-1.960.25981380.20852618275699
1.96-2.010.24731350.1962584271998
2.01-2.060.21211380.19342622276099
2.06-2.110.23821380.189626262764100
2.11-2.170.25061380.181726162754100
2.17-2.240.21221390.18672633277299
2.24-2.320.21641380.171426342772100
2.32-2.420.23181400.188326492789100
2.42-2.530.24281390.191526442783100
2.53-2.660.24321390.19372635277499
2.66-2.830.22571400.185826642804100
2.83-3.050.20421400.18232665280599
3.05-3.350.23311410.179226842825100
3.35-3.840.1651420.157627012843100
3.84-4.830.17131450.133727392884100
4.83-48.640.17721480.16112827297598
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)
13.48021.5927-2.67923.0636-2.48035.61680.09140.26760.17930.10330.1170.1297-0.3125-0.1909-0.19830.19810.0106-0.00130.1873-0.00420.183414.653334.69731.5127
21.32650.94840.33675.3962.08792.34590.16490.1014-0.1623-0.127-0.37010.2313-0.0099-0.35570.18140.18550.04090.00910.4507-0.15090.335616.637522.0013-4.8693
31.58991.22841.18071.00491.22174.9134-0.03830.2928-0.21160.00830.17230.04660.4328-0.0084-0.11560.2555-0.0222-0.00330.2212-0.01760.21875.662614.792533.6109
47.27452.2614-2.61781.195-0.10262.44450.04360.005-0.9860.1048-0.0504-0.62720.31290.31220.03330.24370.0191-0.05920.309-0.06090.519916.93779.34886.2181
52.86730.1493-0.90512.7196-0.26032.87290.0084-0.31120.04360.2256-0.0595-0.00970.04110.17990.06360.2371-0.0125-0.01590.21280.00170.16643.869825.297763.0938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 108 )B3 - 108
2X-RAY DIFFRACTION2chain 'B' and (resid 109 through 211 )B109 - 211
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 116 )A1 - 116
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 220 )A117 - 220
5X-RAY DIFFRACTION5chain 'C' and (resid 20 through 138 )C20 - 138

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