[English] 日本語
Yorodumi
- PDB-1p9m: Crystal structure of the hexameric human IL-6/IL-6 alpha receptor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p9m
TitleCrystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex
Components
  • Interleukin-6
  • Interleukin-6 receptor alpha chain
  • Interleukin-6 receptor beta chain
Keywordssignaling protein/cytokine / Ig domain / four helix bundle / cytokine / interleukin-6 / gp130 / signaling protein-cytokine COMPLEX
Function / homology
Function and homology information


ciliary neurotrophic factor binding / regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / interleukin-6 receptor activity / interleukin-6 binding / negative regulation of primary miRNA processing / ciliary neurotrophic factor receptor activity ...ciliary neurotrophic factor binding / regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / interleukin-6 receptor activity / interleukin-6 binding / negative regulation of primary miRNA processing / ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / regulation of vascular endothelial growth factor production / leukemia inhibitory factor signaling pathway / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / interleukin-27 receptor activity / regulation of microglial cell activation / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / positive regulation of apoptotic DNA fragmentation / positive regulation of type B pancreatic cell apoptotic process / hepatocyte proliferation / response to peptidoglycan / neutrophil apoptotic process / germinal center B cell differentiation / positive regulation of extracellular matrix disassembly / interleukin-6 receptor binding / positive regulation of B cell activation / interleukin-11-mediated signaling pathway / positive regulation of receptor signaling pathway via STAT / T-helper 17 cell lineage commitment / inflammatory response to wounding / positive regulation of T-helper 2 cell cytokine production / endocrine pancreas development / negative regulation of collagen biosynthetic process / positive regulation of adaptive immune response / regulation of neuroinflammatory response / positive regulation of acute inflammatory response / vascular endothelial growth factor production / positive regulation of astrocyte differentiation / negative regulation of interleukin-8 production / negative regulation of chemokine production / T follicular helper cell differentiation / positive regulation of neuroinflammatory response / intestinal epithelial cell development / positive regulation of glomerular mesangial cell proliferation / positive regulation of leukocyte chemotaxis / positive regulation of platelet aggregation / neutrophil mediated immunity / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / positive regulation of cytokine production involved in inflammatory response / Interleukin-35 Signalling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of bone resorption / CD163 mediating an anti-inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immunoglobulin production / Interleukin-6 signaling / growth factor binding / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / maintenance of blood-brain barrier / cytokine binding / MAPK1 (ERK2) activation / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of interleukin-17 production / humoral immune response / protein tyrosine kinase activator activity / positive regulation of vascular endothelial growth factor production / Transcriptional Regulation by VENTX / positive regulation of interleukin-10 production / negative regulation of lipid storage / positive regulation of glial cell proliferation / positive regulation of peptidyl-serine phosphorylation / regulation of angiogenesis / cell surface receptor signaling pathway via JAK-STAT / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / positive regulation of DNA-binding transcription factor activity / coreceptor activity / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / response to cytokine / positive regulation of T cell proliferation / liver regeneration / positive regulation of smooth muscle cell proliferation
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / : / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. ...Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / : / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-6 / Interleukin-6 receptor subunit alpha / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsBoulanger, M.J. / Chow, D.C. / Brevnova, E.E. / Garcia, K.C.
CitationJournal: Science / Year: 2003
Title: Hexameric Structure and Assembly of the Interleukin-6/IL-6 alpha-Receptor/gp130 Complex
Authors: Boulanger, M.J. / Chow, D.C. / Brevnova, E.E. / Garcia, K.C.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-6 receptor beta chain
B: Interleukin-6
C: Interleukin-6 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)78,2533
Polymers78,2533
Non-polymers00
Water00
1
A: Interleukin-6 receptor beta chain
B: Interleukin-6
C: Interleukin-6 receptor alpha chain

A: Interleukin-6 receptor beta chain
B: Interleukin-6
C: Interleukin-6 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)156,5076
Polymers156,5076
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_455y-2/3,x+2/3,-z+2/31
Buried area13030 Å2
ΔGint-67 kcal/mol
Surface area65930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)279.800, 279.800, 96.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Interleukin-6 receptor beta chain / IL-6R-beta / Interleukin 6 signal transducer / Membrane glycoprotein 130 / GP130 / Oncostatin M ...IL-6R-beta / Interleukin 6 signal transducer / Membrane glycoprotein 130 / GP130 / Oncostatin M receptor / CDw130 / CD130 antigen


Mass: 34099.535 Da / Num. of mol.: 1 / Fragment: extracellular domains D1 - D3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6ST / Plasmid: pACGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40189
#2: Protein Interleukin-6 / IL-6 / B-cell stimulatory factor 2 / BSF-2 / Interferon beta-2 / Hybridoma growth factor


Mass: 21103.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6 OR IFNB2 / Plasmid: pACGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05231
#3: Protein Interleukin-6 receptor alpha chain / IL-6R-alpha / IL-6R 1 / CD126 antigen


Mass: 23050.865 Da / Num. of mol.: 1 / Fragment: extracellular domains D2 - D3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6R / Plasmid: pACGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08887
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.65 Å3/Da / Density % sol: 73.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Sodium formate, Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
22.0 Msodium formate1reservoirpH4.5
30.1 Msodium acetate1reservoirpH4.5

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. all: 16144 / Num. obs: 15861 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13
Reflection shellResolution: 3.65→3.84 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.85 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 16144 / Num. measured all: 120957
Reflection shell
*PLUS
% possible obs: 98.1 % / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ALU

1alu


Resolution: 3.65→19.99 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1237 7.8 %RANDOM
Rwork0.282 ---
obs0.282 15767 98.2 %-
all-16061 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.115109 e/Å3
Displacement parametersBiso mean: 117.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å230.66 Å20 Å2
2--2.77 Å20 Å2
3----5.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a1.29 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 3.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 0 0 5322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 3.65→3.88 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.487 185 7.2 %
Rwork0.403 2396 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
LS refinement shell
*PLUS
Rfactor Rfree: 0.494 / Rfactor Rwork: 0.406

+
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