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- PDB-1buy: HUMAN ERYTHROPOIETIN, NMR MINIMIZED AVERAGE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1buy
TitleHUMAN ERYTHROPOIETIN, NMR MINIMIZED AVERAGE STRUCTURE
ComponentsPROTEIN (ERYTHROPOIETIN)
KeywordsCYTOKINE / GLYCOPROTEIN / GROWTH FACTOR
Function / homology
Function and homology information


nucleate erythrocyte development / negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / negative regulation of cation channel activity / erythropoietin-mediated signaling pathway / 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 ...nucleate erythrocyte development / negative regulation of erythrocyte apoptotic process / erythropoietin receptor binding / negative regulation of cation channel activity / erythropoietin-mediated signaling pathway / 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) / cellular hyperosmotic response / 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 testosterone / positive regulation of activated T cell proliferation / response to dexamethasone / protein kinase activator activity / erythrocyte maturation / response to axon injury / response to hyperoxia / response to electrical stimulus / Erythropoietin activates RAS / positive regulation of tyrosine phosphorylation of STAT protein / response to salt stress / positive regulation of neuron differentiation / embryo implantation / response to interleukin-1 / erythrocyte differentiation / cytokine activity / acute-phase response / hormone activity / positive regulation of neuron projection development / response to estrogen / cell body / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular region
Similarity search - Function
Erythropoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING PROTOCOL
AuthorsCheetham, J.C. / Smith, D.M. / Aoki, K.H. / Stevenson, J.L. / Hoeffel, T.J. / Syed, R.S. / Egrie, J. / Harvey, T.S.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: NMR structure of human erythropoietin and a comparison with its receptor bound conformation.
Authors: Cheetham, J.C. / Smith, D.M. / Aoki, K.H. / Stevenson, J.L. / Hoeffel, T.J. / Syed, R.S. / Egrie, J. / Harvey, T.S.
History
DepositionSep 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ERYTHROPOIETIN)


Theoretical massNumber of molelcules
Total (without water)18,4641
Polymers18,4641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -LEAST RESTRAINT VIOLATION
Representative

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Components

#1: 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) / Description: SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P01588

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112/3/4D NOESY
121TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 15N, 13C PROTEIN

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Sample preparation

Sample conditionspH: 6.3 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX500BrukerDRX5005001
Varian DRX600VarianDRX6006002
Varian UNITYPLUSVarianUNITYPLUS6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING PROTOCOL / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers submitted total number: 1

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