+Open data
-Basic information
Entry | Database: PDB / ID: 1i1r | ||||||
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Title | CRYSTAL STRUCTURE OF A CYTOKINE/RECEPTOR COMPLEX | ||||||
Components |
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Keywords | CYTOKINE / cytokine-receptor complex / gp130 / viral IL-6 | ||||||
Function / homology | Function and homology information interleukin-27 receptor activity / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex ...interleukin-27 receptor activity / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / interleukin-6 receptor binding / virus-mediated perturbation of host defense response => GO:0019049 / 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 / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / glycogen metabolic process / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / cytokine binding / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / positive regulation of cardiac muscle hypertrophy / MAPK3 (ERK1) activation / growth factor binding / MAPK1 (ERK2) activation / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / response to cytokine / 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 / dendrite / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 8 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Chow, D. / He, X. / Snow, A.L. / Rose-John, S. / Garcia, K.C. | ||||||
Citation | Journal: 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 |
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Remark 300 | BIOMOLECULE: 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). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i1r.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i1r.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1r ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the 2-fold crystallographic axis |
-Components
#1: Protein | 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 |
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#2: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.77 % | ||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: human Interleukin-6 1ALU, gp130 D2D3 domains 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
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Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.019
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