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- PDB-7ox2: Fab 6E2: hIL-9 complex -

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Basic information

Entry
Database: PDB / ID: 7ox2
TitleFab 6E2: hIL-9 complex
Components
  • Heavy chain (Fab 6E2)
  • Interleukin-9
  • Light chain (Fab 6E2)
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: 3.34 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 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: Heavy chain (Fab 6E2)
L: Light chain (Fab 6E2)
T: Interleukin-9
B: Heavy chain (Fab 6E2)
C: Light chain (Fab 6E2)
O: Interleukin-9
D: Heavy chain (Fab 6E2)
E: Light chain (Fab 6E2)
M: Interleukin-9
J: Heavy chain (Fab 6E2)
K: Light chain (Fab 6E2)
N: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,43017
Polymers240,95012
Non-polymers4805
Water362
1
A: Heavy chain (Fab 6E2)
L: Light chain (Fab 6E2)
T: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3344
Polymers60,2373
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-46 kcal/mol
Surface area24410 Å2
MethodPISA
2
B: Heavy chain (Fab 6E2)
C: Light chain (Fab 6E2)
O: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3344
Polymers60,2373
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-45 kcal/mol
Surface area24120 Å2
MethodPISA
3
D: Heavy chain (Fab 6E2)
E: Light chain (Fab 6E2)
M: Interleukin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5266
Polymers60,2373
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-72 kcal/mol
Surface area24140 Å2
MethodPISA
4
J: Heavy chain (Fab 6E2)
K: Light chain (Fab 6E2)
N: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)60,2373
Polymers60,2373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-31 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.358, 94.364, 107.331
Angle α, β, γ (deg.)82.540, 72.000, 80.790
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))
21(chain B and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))
31(chain D and (resid 1 through 195 or resid 197 through 218))
41(chain J and (resid 1 through 130 or resid 139 through 218))
12(chain C and resid 3 through 211)
22chain E
32chain K
42chain L
13(chain M and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))
23(chain N and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))
33chain O
43(chain T and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNPROPRO(chain A and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))AA1 - 1301 - 130
121THRTHRTHRTHR(chain A and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))AA139 - 195139 - 195
131THRTHRLYSLYS(chain A and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))AA197 - 218197 - 218
211GLNGLNPROPRO(chain B and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))BD1 - 1301 - 130
221THRTHRTHRTHR(chain B and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))BD139 - 195139 - 195
231THRTHRLYSLYS(chain B and (resid 1 through 130 or resid 139 through 195 or resid 197 through 218))BD197 - 218197 - 218
311GLNGLNTHRTHR(chain D and (resid 1 through 195 or resid 197 through 218))DG1 - 1951 - 195
321THRTHRLYSLYS(chain D and (resid 1 through 195 or resid 197 through 218))DG197 - 218197 - 218
411GLNGLNPROPRO(chain J and (resid 1 through 130 or resid 139 through 218))JJ1 - 1301 - 130
421THRTHRLYSLYS(chain J and (resid 1 through 130 or resid 139 through 218))JJ139 - 218139 - 218
112ALAALATHRTHR(chain C and resid 3 through 211)CE3 - 2113 - 211
212ALAALATHRTHRchain EEH3 - 2113 - 211
312ALAALATHRTHRchain KKK3 - 2113 - 211
412ALAALATHRTHRchain LLB3 - 2113 - 211
113CYSCYSPROPRO(chain M and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))MI21 - 607 - 46
123THRTHRPROPRO(chain M and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))MI65 - 11251 - 98
133THRTHRARGARG(chain M and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))MI116 - 138102 - 124
213CYSCYSPROPRO(chain N and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))NL21 - 607 - 46
223THRTHRPROPRO(chain N and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))NL65 - 11251 - 98
233THRTHRARGARG(chain N and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))NL116 - 138102 - 124
313CYSCYSARGARGchain OOF21 - 1387 - 124
413CYSCYSPROPRO(chain T and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))TC21 - 607 - 46
423THRTHRPROPRO(chain T and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))TC65 - 11251 - 98
433THRTHRARGARG(chain T and (resid 21 through 60 or resid 65 through 112 or resid 116 through 138))TC116 - 138102 - 124

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
Heavy chain (Fab 6E2)


Mass: 23045.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Light chain (Fab 6E2)


Mass: 22640.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 4
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.: 2 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 0.2M lithium sulfate, 0.1M phosphate/ citric acid, pH 3.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 3.34→48.92 Å / Num. obs: 34638 / % possible obs: 93.6 % / Redundancy: 2.9 % / CC1/2: 0.96 / Net I/σ(I): 4.78
Reflection shellResolution: 3.34→3.54 Å / Num. unique obs: 5336 / CC1/2: 0.517

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GHG, 5Y9J

6ghg

5y9j


Resolution: 3.34→48.92 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 1728 5 %
Rwork0.2238 32861 -
obs0.2268 34589 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.6 Å2 / Biso mean: 86.319 Å2 / Biso min: 17.63 Å2
Refinement stepCycle: final / Resolution: 3.34→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16132 0 25 2 16159
Biso mean--96.97 25.74 -
Num. residues----2149
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2484X-RAY DIFFRACTION9.232TORSIONAL
12B2484X-RAY DIFFRACTION9.232TORSIONAL
13D2484X-RAY DIFFRACTION9.232TORSIONAL
14J2484X-RAY DIFFRACTION9.232TORSIONAL
21C2516X-RAY DIFFRACTION9.232TORSIONAL
22E2516X-RAY DIFFRACTION9.232TORSIONAL
23K2516X-RAY DIFFRACTION9.232TORSIONAL
24L2516X-RAY DIFFRACTION9.232TORSIONAL
31M1316X-RAY DIFFRACTION9.232TORSIONAL
32N1316X-RAY DIFFRACTION9.232TORSIONAL
33O1316X-RAY DIFFRACTION9.232TORSIONAL
34T1316X-RAY DIFFRACTION9.232TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.34-3.440.45741270.33032410253782
3.44-3.550.32321480.30242812296096
3.55-3.680.35331480.27962818296696
3.68-3.820.3211460.26812794294095
3.82-40.29381450.25442756290195
4-4.210.32431400.23262662280292
4.21-4.470.25741480.19592818296695
4.47-4.820.24571460.18492758290495
4.82-5.30.25691470.19582804295195
5.3-6.060.27871420.21352701284393
6.07-7.640.26231470.20582792293995
7.64-48.920.24081440.19522736288094

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