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- PDB-1eer: CRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPT... -

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Basic information

Entry
Database: PDB / ID: 1eer
TitleCRYSTAL STRUCTURE OF HUMAN ERYTHROPOIETIN COMPLEXED TO ITS RECEPTOR AT 1.9 ANGSTROMS
Components
  • ERYTHROPOIETIN
  • ERYTHROPOIETIN RECEPTOR
KeywordsCOMPLEX (CYTOKINE/RECEPTOR) / ERYTHROPOIETIN / ERYTHROPOIETIN RECEPTOR / SIGNAL TRANSDUCTION / HEMATOPOIETIC CYTOKINE / CYTOKINE RECEPTOR CLASS 1 / COMPLEX (CYTOKINE-RECEPTOR) / COMPLEX (CYTOKINE-RECEPTOR) complex
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 / embryo implantation / positive regulation of neuron differentiation / 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 / MIRAS / Resolution: 1.9 Å
AuthorsSyed, R.S. / Li, C.
CitationJournal: 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.
History
DepositionJul 24, 1998Processing site: BNL
Revision 1.0Oct 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: ERYTHROPOIETIN
B: ERYTHROPOIETIN RECEPTOR
C: ERYTHROPOIETIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)68,8443
Polymers68,8443
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.400, 79.300, 136.500
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 ERYTHROPOIETIN


Mass: 18471.289 Da / Num. of mol.: 1 / Mutation: N24K, N38K, N83K, P121N, P122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01588
#2: Protein ERYTHROPOIETIN RECEPTOR / EPOBP


Mass: 25186.449 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
132 %PEG15001reservoir
20.28 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 49480 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.377 / % possible all: 82.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Num. measured all: 251681 / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 23.5 Å2
Reflection shell
*PLUS
% possible obs: 82.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→50 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1329 3 %RANDOM
Rwork0.242 ---
obs0.242 44507 93.3 %-
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 0 298 4917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.66
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3543 106 2.2 %
Rwork0.2428 3536 -
obs--73.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66

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