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- PDB-1i1r: CRYSTAL STRUCTURE OF A CYTOKINE/RECEPTOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i1r
TitleCRYSTAL STRUCTURE OF A CYTOKINE/RECEPTOR COMPLEX
Components
  • INTERLEUKIN-6 RECEPTOR BETA CHAIN
  • VIRAL IL-6
KeywordsCYTOKINE / cytokine-receptor complex / gp130 / viral IL-6
Function / homology
Function and homology information


ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / leukemia inhibitory factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / interleukin-27 receptor activity / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding ...ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / leukemia inhibitory factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / interleukin-27 receptor activity / 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 / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of adaptive immune response / positive regulation of acute inflammatory response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / positive regulation of platelet aggregation / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / Interleukin-35 Signalling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / 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 / MAPK3 (ERK1) activation / cytokine binding / MAPK1 (ERK2) activation / protein tyrosine kinase activator activity / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / coreceptor activity / response to cytokine / positive regulation of T cell proliferation / cytokine activity / cytokine-mediated signaling pathway / scaffold protein binding / negative regulation of neuron apoptotic process / receptor complex / immune response / membrane raft / external side of plasma membrane / neuronal cell body / positive regulation of cell population proliferation / dendrite / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / : / Type I cytokine receptor, cytokine-binding domain / 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 ...Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / : / Type I cytokine receptor, cytokine-binding domain / 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; / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-6 receptor subunit beta / Interleukin-6 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChow, D. / He, X. / Snow, A.L. / Rose-John, S. / Garcia, K.C.
CitationJournal: Science / Year: 2001
Title: Structure of an extracellular gp130 cytokine receptor signaling complex.
Authors: Chow, D. / He, X. / Snow, A.L. / Rose-John, S. / Garcia, K.C.
History
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL ASSEMBLY IS A TETRAMER, OF WHICH HALF (ONE VIL-6, ONE GP130) IS IN THE ASYMMETRIC UNIT. THE DYAD-AXIS OF THE TETRAMER IS THE C2 CRYSTALLOGRAPHIC AXIS. NOTE: COORDINATES FOR THE ENTIRE TETRAMER CAN BE OBTAINED DIRECTLY FROM THE AUTHORS (kcgarcia@stanford.edu).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-6 RECEPTOR BETA CHAIN
B: VIRAL IL-6


Theoretical massNumber of molelcules
Total (without water)55,5212
Polymers55,5212
Non-polymers00
Water6,666370
1
A: INTERLEUKIN-6 RECEPTOR BETA CHAIN
B: VIRAL IL-6

A: INTERLEUKIN-6 RECEPTOR BETA CHAIN
B: VIRAL IL-6


Theoretical massNumber of molelcules
Total (without water)111,0434
Polymers111,0434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)103.000, 123.310, 76.790
Angle α, β, γ (deg.)90.00, 112.03, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the 2-fold crystallographic axis

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Components

#1: Protein INTERLEUKIN-6 RECEPTOR BETA CHAIN / GP130


Mass: 34664.105 Da / Num. of mol.: 1
Fragment: DOMAINS 1, 2, 3 OF THE GP130 EXTRACELLULAR DOMAIN (RESIDUES 1-303)
Source method: isolated from a genetically manipulated source
Details: EXPRESSED IN THE PRESENCE OF INHIBITOR OF N-LINKED GLYCOSYLATION (TUNICAMYCIN)
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40189
#2: Protein VIRAL IL-6 / FUNCTIONAL INTERLEUKIN-6 HOMOLOG


Mass: 20857.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NON-GLYCOSYLATED / Source: (gene. exp.) Human herpesvirus 8 / Genus: Rhadinovirus / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q98823
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPEG 2000, sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
210 %mPEG200011
30.1 MNa citrate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 34376 / Num. obs: 34376 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 3.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3420 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 106397
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human Interleukin-6 1ALU, gp130 D2D3 domains 1BQU

1alu

1bqu


Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: wilson B value 50.2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3425 -RANDOM
Rwork0.213 ---
all0.213 34376 --
obs0.213 34376 100 %-
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å213.53 Å2-13.12 Å2
2--0 Å2-5.74 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 0 370 4153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.349 353 -
Rwork0.321 --
obs-3420 99.5 %

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