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- PDB-1alu: HUMAN INTERLEUKIN-6 -

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Basic information

Entry
Database: PDB / ID: 1alu
TitleHUMAN INTERLEUKIN-6
ComponentsINTERLEUKIN-6
KeywordsCYTOKINE / INTERLEUKIN / RECEPTOR / SIGNALING / GLYCOPROTEIN
Function / homology
Function and homology information


regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of primary miRNA processing / regulation of vascular endothelial growth factor production / negative regulation of interleukin-1-mediated signaling pathway / regulation of microglial cell activation / interleukin-6 receptor complex ...regulation of astrocyte activation / glucagon secretion / positive regulation of interleukin-21 production / regulation of glucagon secretion / hepatic immune response / negative regulation of primary miRNA processing / regulation of vascular endothelial growth factor production / negative regulation of interleukin-1-mediated signaling pathway / regulation of microglial cell activation / interleukin-6 receptor complex / positive regulation of apoptotic DNA fragmentation / hepatocyte proliferation / positive regulation of type B pancreatic cell apoptotic process / 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 / 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 / regulation of neuroinflammatory response / positive regulation of acute inflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / T follicular helper cell differentiation / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / positive regulation of platelet aggregation / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / 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 / interleukin-6-mediated signaling pathway / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / maintenance of blood-brain barrier / MAPK1 (ERK2) activation / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of interleukin-17 production / humoral immune response / positive regulation of vascular endothelial growth factor production / Transcriptional Regulation by VENTX / positive regulation of interleukin-10 production / positive regulation of glial cell proliferation / negative regulation of lipid storage / 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 / positive regulation of chemokine production / positive regulation of T cell proliferation / liver regeneration / positive regulation of smooth muscle cell proliferation / regulation of insulin secretion / response to glucocorticoid / positive regulation of translation / positive regulation of interleukin-1 beta production / cytokine activity / acute-phase response / response to activity / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / growth factor activity / neuron cellular homeostasis / cellular response to virus / platelet activation / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / cellular response to hydrogen peroxide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / neuron projection development / positive regulation of tumor necrosis factor production / ADORA2B mediated anti-inflammatory cytokines production / glucose homeostasis / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / defense response to virus / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / positive regulation of apoptotic process / endoplasmic reticulum lumen / inflammatory response
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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Interleukin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsSomers, W.S. / Stahl, M. / Seehra, J.S.
CitationJournal: EMBO J. / Year: 1997
Title: 1.9 A crystal structure of interleukin 6: implications for a novel mode of receptor dimerization and signaling.
Authors: Somers, W. / Stahl, M. / Seehra, J.S.
History
DepositionJun 3, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6716
Polymers21,1371
Non-polymers5345
Water2,162120
1
A: INTERLEUKIN-6
hetero molecules

A: INTERLEUKIN-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,34312
Polymers42,2742
Non-polymers1,06910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
MethodPQS
2
A: INTERLEUKIN-6
hetero molecules

A: INTERLEUKIN-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,34312
Polymers42,2742
Non-polymers1,06910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3870 Å2
ΔGint-127 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.678, 49.678, 121.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein INTERLEUKIN-6


Mass: 21137.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05231
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.3
Details: PROTEIN AT 15 MG/ML WAS CRYSTALLIZED FROM 1.8M AMMONIUM SULFATE, 300 MM SODIUM POTASSIUM TARTRATE, IN 100MM PH 6.3 SODIUM CITRATE BUFFER.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
2300 mMsodium potassium tartrate1reservoir
3100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 14002 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.129 / % possible all: 88.5
Reflection
*PLUS
Num. measured all: 100519
Reflection shell
*PLUS
% possible obs: 88.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
MLPHAREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 -5 %RANDOM
Rwork0.213 ---
obs-13905 98 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 30 120 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.026
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it3.3
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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