[English] 日本語
Yorodumi
- PDB-7ox1: Fab 7D6: hIL-9 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ox1
TitleFab 7D6: hIL-9 complex
Components
  • Heavy chain (Fab 7D6)
  • Interleukin-9Interleukin 9
  • Light chain (Fab 7D6)
KeywordsCYTOKINE / IL-9 / complex
Function / homology
Function and homology information


interleukin-9 receptor binding / Interleukin-9 signaling / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity / growth factor activity ...interleukin-9 receptor binding / Interleukin-9 signaling / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / 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.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more