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- PDB-7ox1: Fab 7D6: hIL-9 complex -

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Basic information

Entry
Database: PDB / ID: 7ox1
TitleFab 7D6: hIL-9 complex
Components
  • Heavy chain (Fab 7D6)
  • Interleukin-9
  • Light chain (Fab 7D6)
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: 2.49 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain (Fab 7D6)
B: Light chain (Fab 7D6)
C: Heavy chain (Fab 7D6)
D: Light chain (Fab 7D6)
E: Heavy chain (Fab 7D6)
F: Light chain (Fab 7D6)
G: Interleukin-9
H: Heavy chain (Fab 7D6)
L: Light chain (Fab 7D6)
X: Interleukin-9
Y: Interleukin-9
Z: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)246,77412
Polymers246,77412
Non-polymers00
Water4,053225
1
A: Heavy chain (Fab 7D6)
B: Light chain (Fab 7D6)
G: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)61,6933
Polymers61,6933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heavy chain (Fab 7D6)
D: Light chain (Fab 7D6)
Z: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)61,6933
Polymers61,6933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Heavy chain (Fab 7D6)
F: Light chain (Fab 7D6)
Y: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)61,6933
Polymers61,6933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Heavy chain (Fab 7D6)
L: Light chain (Fab 7D6)
X: Interleukin-9


Theoretical massNumber of molelcules
Total (without water)61,6933
Polymers61,6933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.350, 102.750, 164.370
Angle α, β, γ (deg.)90.000, 94.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 229)
21(chain C and (resid 1 through 140 or resid 149 through 229))
31(chain E and (resid 1 through 140 or resid 149 through 229))
41(chain H and (resid 1 through 140 or resid 149 through 229))
12(chain B and (resid 2 through 104 or resid 106...
22(chain D and (resid 2 through 104 or resid 106...
32(chain F and (resid 2 through 104 or resid 106 through 191 or resid 196 through 205))
42(chain L and (resid 2 through 104 or resid 106...
13(chain G and (resid 20 through 46 or resid 55...
23(chain X and (resid 20 through 62 or resid 66 through 108 or resid 111 or resid 119 through 140))
33(chain Y and (resid 20 through 46 or resid 55 through 115 or resid 119 through 140))
43(chain Z and (resid 20 through 46 or resid 55...

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
111GLNGLNSERSER(chain A and resid 1 through 229)AA1 - 2291 - 229
211GLNGLNPROPRO(chain C and (resid 1 through 140 or resid 149 through 229))CC1 - 1401 - 140
221THRTHRSERSER(chain C and (resid 1 through 140 or resid 149 through 229))CC149 - 229149 - 229
311GLNGLNPROPRO(chain E and (resid 1 through 140 or resid 149 through 229))EE1 - 1401 - 140
321THRTHRSERSER(chain E and (resid 1 through 140 or resid 149 through 229))EE149 - 229149 - 229
411GLNGLNPROPRO(chain H and (resid 1 through 140 or resid 149 through 229))HH1 - 1401 - 140
421THRTHRSERSER(chain H and (resid 1 through 140 or resid 149 through 229))HH149 - 229149 - 229
112ALAALATHRTHR(chain B and (resid 2 through 104 or resid 106...BB2 - 1042 - 104
122LEULEUALAALA(chain B and (resid 2 through 104 or resid 106...BB106 - 150106 - 150
132ALAALAVALVAL(chain B and (resid 2 through 104 or resid 106...BB2 - 2092 - 209
212ALAALATHRTHR(chain D and (resid 2 through 104 or resid 106...DD2 - 1042 - 104
222LEULEUALAALA(chain D and (resid 2 through 104 or resid 106...DD106 - 150106 - 150
232SERSERTYRTYR(chain D and (resid 2 through 104 or resid 106...DD155 - 180155 - 180
242THRTHRHISHIS(chain D and (resid 2 through 104 or resid 106...DD184 - 191184 - 191
252CYSCYSVALVAL(chain D and (resid 2 through 104 or resid 106...DD196 - 205196 - 205
312ALAALATHRTHR(chain F and (resid 2 through 104 or resid 106 through 191 or resid 196 through 205))FF2 - 1042 - 104
322LEULEUHISHIS(chain F and (resid 2 through 104 or resid 106 through 191 or resid 196 through 205))FF106 - 191106 - 191
332CYSCYSVALVAL(chain F and (resid 2 through 104 or resid 106 through 191 or resid 196 through 205))FF196 - 205196 - 205
412ALAALATHRTHR(chain L and (resid 2 through 104 or resid 106...LI2 - 1042 - 104
422LEULEUALAALA(chain L and (resid 2 through 104 or resid 106...LI106 - 150106 - 150
432SERSERTYRTYR(chain L and (resid 2 through 104 or resid 106...LI155 - 180155 - 180
442THRTHRHISHIS(chain L and (resid 2 through 104 or resid 106...LI184 - 191184 - 191
452CYSCYSVALVAL(chain L and (resid 2 through 104 or resid 106...LI196 - 205196 - 205
113GLYGLYHISHIS(chain G and (resid 20 through 46 or resid 55...GG20 - 466 - 32
123LEULEUASPASP(chain G and (resid 20 through 46 or resid 55...GG55 - 6241 - 48
133ARGARGSERSER(chain G and (resid 20 through 46 or resid 55...GG66 - 10852 - 94
143GLNGLNGLNGLN(chain G and (resid 20 through 46 or resid 55...GG11197
153GLYGLYMETMET(chain G and (resid 20 through 46 or resid 55...GG119 - 140105 - 126
213GLYGLYASPASP(chain X and (resid 20 through 62 or resid 66 through 108 or resid 111 or resid 119 through 140))XJ20 - 626 - 48
223ARGARGSERSER(chain X and (resid 20 through 62 or resid 66 through 108 or resid 111 or resid 119 through 140))XJ66 - 10852 - 94
233GLNGLNGLNGLN(chain X and (resid 20 through 62 or resid 66 through 108 or resid 111 or resid 119 through 140))XJ11197
243GLYGLYMETMET(chain X and (resid 20 through 62 or resid 66 through 108 or resid 111 or resid 119 through 140))XJ119 - 140105 - 126
313GLYGLYHISHIS(chain Y and (resid 20 through 46 or resid 55 through 115 or resid 119 through 140))YK20 - 466 - 32
323LEULEUGLNGLN(chain Y and (resid 20 through 46 or resid 55 through 115 or resid 119 through 140))YK55 - 11541 - 101
333GLYGLYMETMET(chain Y and (resid 20 through 46 or resid 55 through 115 or resid 119 through 140))YK119 - 140105 - 126
413GLYGLYHISHIS(chain Z and (resid 20 through 46 or resid 55...ZL20 - 466 - 32
423LEULEUASPASP(chain Z and (resid 20 through 46 or resid 55...ZL55 - 6241 - 48
433ARGARGSERSER(chain Z and (resid 20 through 46 or resid 55...ZL66 - 10852 - 94
443GLNGLNGLNGLN(chain Z and (resid 20 through 46 or resid 55...ZL11197
453GLYGLYMETMET(chain Z and (resid 20 through 46 or resid 55...ZL119 - 140105 - 126

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
Heavy chain (Fab 7D6)


Mass: 24484.410 Da / Num. of mol.: 4
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
Light chain (Fab 7D6)


Mass: 22657.975 Da / Num. of mol.: 4
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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.25M ammonium nitrate, 18% PEG 3350, 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.49→42.36 Å / Num. obs: 92495 / % possible obs: 97.7 % / Redundancy: 3.2 % / CC1/2: 0.997 / Net I/σ(I): 11.99
Reflection shellResolution: 2.49→2.64 Å / Num. unique obs: 14578 / CC1/2: 0.495

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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: 4HC1, 4R90

4hc1

4r90


Resolution: 2.49→42.36 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 4624 5 %
Rwork0.2092 87856 -
obs0.2118 92480 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 327.71 Å2 / Biso mean: 78.2642 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 2.49→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16269 0 0 225 16494
Biso mean---52.14 -
Num. residues----2157
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2652X-RAY DIFFRACTION11.72TORSIONAL
12C2652X-RAY DIFFRACTION11.72TORSIONAL
13E2652X-RAY DIFFRACTION11.72TORSIONAL
14H2652X-RAY DIFFRACTION11.72TORSIONAL
21B2256X-RAY DIFFRACTION11.72TORSIONAL
22D2256X-RAY DIFFRACTION11.72TORSIONAL
23F2256X-RAY DIFFRACTION11.72TORSIONAL
24L2256X-RAY DIFFRACTION11.72TORSIONAL
31G1172X-RAY DIFFRACTION11.72TORSIONAL
32X1172X-RAY DIFFRACTION11.72TORSIONAL
33Y1172X-RAY DIFFRACTION11.72TORSIONAL
34Z1172X-RAY DIFFRACTION11.72TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.520.39011300.33632468259883
2.52-2.550.35451550.31722964311999
2.55-2.580.34311560.29942949310599
2.58-2.610.42981550.29582948310399
2.61-2.650.31561540.28482937309199
2.65-2.680.30361560.28232963311999
2.68-2.720.33061570.26982973313099
2.72-2.760.32921530.26462916306999
2.76-2.80.30661570.2462976313399
2.8-2.850.28821570.24572987314499
2.85-2.90.30471550.24972942309799
2.9-2.950.29981550.2482936309199
2.95-3.010.28861550.25352960311599
3.01-3.070.33651550.25782947310299
3.07-3.140.28081570.24212964312199
3.14-3.210.29641560.22652968312499
3.21-3.290.23331540.21952936309099
3.29-3.380.28141570.22142975313299
3.38-3.480.31861530.22512906305998
3.48-3.590.32391550.22112949310499
3.59-3.720.26541560.21872966312298
3.72-3.870.26281540.20692928308298
3.87-4.040.23481490.18352819296894
4.04-4.260.2691380.18112632277088
4.26-4.520.21071530.17042895304896
4.52-4.870.21171560.15392972312899
4.87-5.360.19631580.16373001315999
5.36-6.130.25081580.19233002316099
6.13-7.720.24441600.199930373197100
7.72-42.360.19131600.17443040320098

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