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- PDB-1cn4: ERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOI... -

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Basic information

Entry
Database: PDB / ID: 1cn4
TitleERYTHROPOIETIN COMPLEXED WITH EXTRACELLULAR DOMAINS OF ERYTHROPOIETIN RECEPTOR
Components
  • PROTEIN (ERYTHROPOIETIN RECEPTOR)
  • PROTEIN (ERYTHROPOIETIN)
KeywordsHEMATOPOIETIC CYTOKINE / CYTOKINE RECEPTOR
Function / homology
Function and homology information


negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / myeloid cell apoptotic process / hemoglobin biosynthetic process / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / negative regulation of calcium ion transport into cytosol / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) ...negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / erythropoietin receptor activity / myeloid cell apoptotic process / hemoglobin biosynthetic process / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / negative regulation of calcium ion transport into cytosol / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / erythropoietin-mediated signaling pathway / cellular hyperosmotic response / cell surface receptor signaling pathway via STAT / response to vitamin A / positive regulation of Ras protein signal transduction / blood circulation / Regulation of gene expression by Hypoxia-inducible Factor / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / response to dexamethasone / erythrocyte maturation / response to testosterone / positive regulation of activated T cell proliferation / decidualization / response to electrical stimulus / protein kinase activator activity / response to hyperoxia / response to axon injury / Erythropoietin activates RAS / response to salt stress / positive regulation of neuron differentiation / embryo implantation / response to interleukin-1 / cytokine activity / erythrocyte differentiation / acute-phase response / positive regulation of neuron projection development / hormone activity / brain development / response to estrogen / cytokine-mediated signaling pathway / heart development / cell body / response to lipopolysaccharide / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. ...Erythropoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain 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
Erythropoietin / Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.8 Å
AuthorsStroud, R.M. / Reid, S.W.
Citation
Journal: Nature / Year: 1998
Title: Efficiency of signalling through cytokine receptors depends critically on receptor orientation.
Authors: Syed, R.S. / Reid, S.W. / Li, C. / Cheetham, J.C. / Aoki, K.H. / Liu, B. / Zhan, H. / Osslund, T.D. / Chirino, A.J. / Zhang, J. / Finer-Moore, J. / Elliott, S. / Sitney, K. / Katz, B.A. / ...Authors: Syed, R.S. / Reid, S.W. / Li, C. / Cheetham, J.C. / Aoki, K.H. / Liu, B. / Zhan, H. / Osslund, T.D. / Chirino, A.J. / Zhang, J. / Finer-Moore, J. / Elliott, S. / Sitney, K. / Katz, B.A. / Matthews, D.J. / Wendoloski, J.J. / Egrie, J. / Stroud, R.M.
#1: Journal: Protein Eng. / Year: 1999
Title: Engineering a Soluble Extracellular Erythropoietin Receptor (EPObp) in Pichia pastoris to Eliminate Microheterogeneity, and its Complex with Erythropoietin
Authors: Zhan, H. / Liu, B. / Reid, S.W. / Aoki, K.H. / Li, C. / Syed, R.S. / Karkaria, C. / Koe, G. / Sitney, K. / Hayenga, K. / Mistry, F. / Savel, L. / Dreyer, M. / Katz, B. / Schreurs, J. / ...Authors: Zhan, H. / Liu, B. / Reid, S.W. / Aoki, K.H. / Li, C. / Syed, R.S. / Karkaria, C. / Koe, G. / Sitney, K. / Hayenga, K. / Mistry, F. / Savel, L. / Dreyer, M. / Katz, B. / Schreurs, J. / Matthews, D.J. / Cheetham, J.C. / Egrie, J. / Giebel, L.B. / Stroud, R.M.
History
DepositionMay 25, 1999Deposition site: BNL / Processing site: RCSB
SupersessionAug 11, 1999ID: 1BLW
Revision 1.0Aug 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ERYTHROPOIETIN RECEPTOR)
B: PROTEIN (ERYTHROPOIETIN RECEPTOR)
C: PROTEIN (ERYTHROPOIETIN)


Theoretical massNumber of molelcules
Total (without water)69,0113
Polymers69,0113
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.340, 80.340, 134.900
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 PROTEIN (ERYTHROPOIETIN RECEPTOR)


Mass: 25273.570 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR LIGAND BINDING DOMAINS / Mutation: N52Q, N164Q, A211E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P19235
#2: Protein PROTEIN (ERYTHROPOIETIN)


Mass: 18464.338 Da / Num. of mol.: 1 / Mutation: N24K, N38K, N83K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01588
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG40001reservoir
20.2 M1reservoirCaCl2
30.1 MMES1reservoirpH6.5-7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 20677 / % possible obs: 91.6 % / Redundancy: 4.3 % / Biso Wilson estimate: -0.2 Å2 / Rsym value: 0.122 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.374 / % possible all: 89
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 91.6 % / Num. measured all: 88794 / Rmerge(I) obs: 0.122
Reflection shell
*PLUS
% possible obs: 89.2 % / Rmerge(I) obs: 0.374

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
MLPHAREphasing
SOLOMONphasing
CNS0.4refinement
bioteXdata scaling
RefinementMethod to determine structure: SIR / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high rms absF: 2899584.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.336 1146 6.8 %RANDOM
Rwork0.28 ---
obs0.28 16861 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.168 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a1.27 Å1.13 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 0 15 4604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 61 2.9 %
Rwork0.431 2057 -
obs--64.2 %
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PARA / Topol file: CNS_TOPPAR:PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 80 Å / Num. reflection obs: 18797 / Rfactor obs: 0.19 / Rfactor Rwork: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.406 / Rfactor Rwork: 0.431

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