[English] 日本語
Yorodumi
- PDB-6o4o: The structure of human interleukin 11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o4o
TitleThe structure of human interleukin 11
ComponentsInterleukin-11Interleukin 11
KeywordsPROTEIN BINDING / cytokine / interleukin / interleukin 11
Function / homology
Function and homology information


interleukin-11 receptor binding / megakaryocyte differentiation / negative regulation of hormone secretion / interleukin-11-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / fat cell differentiation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of peptidyl-tyrosine phosphorylation ...interleukin-11 receptor binding / megakaryocyte differentiation / negative regulation of hormone secretion / interleukin-11-mediated signaling pathway / IL-6-type cytokine receptor ligand interactions / fat cell differentiation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMetcalfe, R.D. / Griffin, M.D.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The structure of the extracellular domains of human interleukin 11 alpha receptor reveals mechanisms of cytokine engagement.
Authors: Metcalfe, R.D. / Aizel, K. / Zlatic, C.O. / Nguyen, P.M. / Morton, C.J. / Lio, D.S. / Cheng, H.C. / Dobson, R.C.J. / Parker, M.W. / Gooley, P.R. / Putoczki, T.L. / Griffin, M.D.W.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4053
Polymers18,2731
Non-polymers1322
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.020, 133.762, 27.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Interleukin-11 / Interleukin 11 / IL-11 / Adipogenesis inhibitory factor / AGIF


Mass: 18273.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20809
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.94 Å3/Da / Density % sol: 36.63 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 18% PEG 3350, 0.1 M Bis-Tris propane pH 9, 0.2 M ammonium sulphate, 0.05 M praseodymium chloride, seeded

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.62→44.59 Å / Num. obs: 18978 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.023 / Rrim(I) all: 0.081 / Net I/σ(I): 16.2
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 918 / CC1/2: 0.74 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHL

4mhl


Resolution: 1.62→37.459 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 908 4.8 %RANDOM
Rwork0.176 ---
obs0.1775 18924 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→37.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1287 0 6 145 1438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011354
X-RAY DIFFRACTIONf_angle_d1.3571851
X-RAY DIFFRACTIONf_dihedral_angle_d12.554839
X-RAY DIFFRACTIONf_chiral_restr0.05215
X-RAY DIFFRACTIONf_plane_restr0.007242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.72150.26651520.20952926X-RAY DIFFRACTION100
1.7215-1.85440.22471520.19922936X-RAY DIFFRACTION100
1.8544-2.0410.24591360.18332961X-RAY DIFFRACTION100
2.041-2.33630.18691500.15982984X-RAY DIFFRACTION100
2.3363-2.94330.17671550.17863030X-RAY DIFFRACTION100
2.9433-37.46870.21731630.17283179X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.1701 Å / Origin y: 16.2098 Å / Origin z: -7.025 Å
111213212223313233
T0.2047 Å2-0.0337 Å20.0414 Å2-0.1738 Å2-0.0113 Å2--0.1949 Å2
L0.6745 °20.7694 °20.1174 °2-1.4937 °20.2443 °2--1.0765 °2
S-0.1634 Å °0.0615 Å °-0.1312 Å °-0.1567 Å °0.1297 Å °-0.182 Å °0.0759 Å °0.0384 Å °-0.0217 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 31:178 )

+
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