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- PDB-2mv6: Solution structure of the transmembrane domain and the juxta-memb... -

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Basic information

Entry
Database: PDB / ID: 2mv6
TitleSolution structure of the transmembrane domain and the juxta-membrane domain of the Erythropoietin Receptor in micelles
ComponentsErythropoietin receptor
KeywordsMEMBRANE PROTEIN / Micelles / Transmembrane domain / Erythropoietin receptor
Function / homology
Function and homology information


erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway ...erythropoietin receptor activity / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hemopoiesis / decidualization / Erythropoietin activates RAS / brain development / cytokine-mediated signaling pathway / heart development / nuclear speck / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Erythropoietin receptor / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Erythropoietin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLi, Q. / Wong, Y. / Huang, Q. / Kang, C.
CitationJournal: Biophys.J. / Year: 2014
Title: Structural insight into the transmembrane domain and the juxtamembrane region of the erythropoietin receptor in micelles.
Authors: Li, Q. / Wong, Y.L. / Huang, Q. / Kang, C.
History
DepositionSep 23, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythropoietin receptor


Theoretical massNumber of molelcules
Total (without water)5,4491
Polymers5,4491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Erythropoietin receptor / EPO-R


Mass: 5448.700 Da / Num. of mol.: 1 / Fragment: UNP residues 237-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPOR / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P19235

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-15N HSQC
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HNCA
1623D HBHA(CO)NH
1723D 1H-15N NOESY
1812D 1H-15N HSQC
1923D HNCO
11023D HCACO

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 10 v/v D2O, 250 mM DPC, 0.5 mM [U-99% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] protein, 10 % D2O, 20 mM sodium phosphate, 200-400 mM DPC, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMsodium phosphate-11
10 v/vD2O-21
250 mMDPC-31
0.5 mMentity-4[U-99% 15N]1
mMentity-5[U-100% 13C; U-100% 15N]0.5-12
10 %D2O-62
20 mMsodium phosphate-72
mMDPC-8200-4002
1 mMDTT-92
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
TopSpinBruker Biospincollection
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: simulated annealing was started with 3500 and cool down to 100 K with 15,000 steps. Structure was energy minimized with powell energy minimization.
NMR constraintsNOE constraints total: 260 / NOE intraresidue total count: 78 / NOE long range total count: 0 / NOE medium range total count: 42 / NOE sequential total count: 140 / Hydrogen bond constraints total count: 17 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 40
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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