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- PDB-1pvh: Crystal structure of leukemia inhibitory factor in complex with gp130 -

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Basic information

Entry
Database: PDB / ID: 1pvh
TitleCrystal structure of leukemia inhibitory factor in complex with gp130
Components
  • Interleukin-6 receptor beta chain
  • Leukemia inhibitory factor
Keywordssignaling protein/cytokine / cytokine / receptor / signaling / beta sheet / four helix bundle / signaling protein-cytokine COMPLEX
Function / homology
Function and homology information


leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / negative regulation of meiotic nuclear division / interleukin-27 receptor activity / muscle organ morphogenesis / cell surface receptor signaling pathway via STAT / oncostatin-M receptor complex / interleukin-11 receptor activity ...leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / negative regulation of meiotic nuclear division / interleukin-27 receptor activity / muscle organ morphogenesis / cell surface receptor signaling pathway via STAT / 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 / lung vasculature development / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation of hormone secretion / trophoblast giant cell differentiation / positive regulation of peptidyl-serine phosphorylation of STAT protein / interleukin-11-mediated signaling pathway / lung lobe morphogenesis / T-helper 17 cell lineage commitment / positive regulation of adaptive immune response / positive regulation of macrophage differentiation / 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 / positive regulation of cell adhesion mediated by integrin / lung alveolus development / 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 / regulation of cell differentiation / MAPK3 (ERK1) activation / growth factor binding / Interleukin-10 signaling / somatic stem cell population maintenance / MAPK1 (ERK2) activation / macrophage differentiation / decidualization / neuron development / positive regulation of vascular endothelial growth factor production / blood vessel remodeling / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / embryo implantation / positive regulation of T cell proliferation / cytokine activity / response to cytokine / stem cell differentiation / growth factor activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / cytokine-mediated signaling pathway / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / gene expression / fibroblast proliferation / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / response to hypoxia / receptor complex / immune response / membrane raft / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / dendrite / neuronal cell body / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Leukemia inhibitory factor / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain ...Leukemia inhibitory factor / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / 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 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Leukemia inhibitory factor / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBoulanger, M.J. / Bankovich, A.J. / Kortemme, T. / Baker, D. / Garcia, K.C.
CitationJournal: Mol.Cell / Year: 2003
Title: Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130.
Authors: Boulanger, M.J. / Bankovich, A.J. / Kortemme, T. / Baker, D. / Garcia, K.C.
History
DepositionJun 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 receptor beta chain
B: Leukemia inhibitory factor
C: Interleukin-6 receptor beta chain
D: Leukemia inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6916
Polymers83,4374
Non-polymers2542
Water3,459192
1
A: Interleukin-6 receptor beta chain
B: Leukemia inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8453
Polymers41,7192
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Interleukin-6 receptor beta chain
D: Leukemia inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8453
Polymers41,7192
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.710, 86.700, 146.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 23069.916 Da / Num. of mol.: 2 / Fragment: domains D2 and D3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6ST / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40189
#2: Protein Leukemia inhibitory factor / / LIF / Differentiation-stimulating factor / D factor / Melanoma-derived LPL inhibitor / MLPLI


Mass: 18648.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIF OR HILDA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P15018
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, Sodium iodide, Imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
28-10 %PEG33501reservoir
30.2 Msodium iodide1reservoir
40.1 Mimidazole1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 35908 / Num. obs: 32573 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.63 Å / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.5 / % possible all: 78.4
Reflection
*PLUS
Num. obs: 35908 / % possible obs: 91 % / Num. measured all: 463823
Reflection shell
*PLUS
% possible obs: 78.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LIF - PDB ENTRY 1LKI, GP130 - PDB ENTRY 1I1R

1lki

1i1r


Resolution: 2.5→39.86 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2616 8 %RANDOM
Rwork0.248 ---
obs0.248 32566 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.8599 Å2 / ksol: 0.316798 e/Å3
Displacement parametersBiso mean: 53.3 Å2
Baniso -1Baniso -2Baniso -3
1--20.48 Å20 Å20 Å2
2--20.61 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 0 2 192 6026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 379 8.2 %
Rwork0.366 4257 -
obs--79 %
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
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.415 / Rfactor Rwork: 0.374

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