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- PDB-2n7i: NMR structure of the prolactin receptor transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 2n7i
TitleNMR structure of the prolactin receptor transmembrane domain
ComponentsProlactin receptor
KeywordsHORMONE RECEPTOR / transmembrane domain / membrane protein / receptor
Function / homology
Function and homology information


prolactin receptor activity / regulation of epithelial cell differentiation / prostate gland growth / mammary gland epithelial cell differentiation / steroid biosynthetic process / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / activation of transmembrane receptor protein tyrosine kinase activity / Prolactin receptor signaling / cytokine binding ...prolactin receptor activity / regulation of epithelial cell differentiation / prostate gland growth / mammary gland epithelial cell differentiation / steroid biosynthetic process / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / activation of transmembrane receptor protein tyrosine kinase activity / Prolactin receptor signaling / cytokine binding / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / mammary gland alveolus development / regulation of cell adhesion / Growth hormone receptor signaling / positive regulation of B cell proliferation / positive regulation of protein autophosphorylation / lactation / embryo implantation / endosome lumen / response to bacterium / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / receptor complex / external side of plasma membrane / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model6
AuthorsBugge, K. / Kragelund, B.B.
CitationJournal: Nat Commun / Year: 2016
Title: A combined computational and structural model of the full-length human prolactin receptor.
Authors: Bugge, K. / Papaleo, E. / Haxholm, G.W. / Hopper, J.T. / Robinson, C.V. / Olsen, J.G. / Lindorff-Larsen, K. / Kragelund, B.B.
History
DepositionSep 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prolactin receptor


Theoretical massNumber of molelcules
Total (without water)3,9611
Polymers3,9611
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Prolactin receptor / PRL-R


Mass: 3960.745 Da / Num. of mol.: 1 / Fragment: Helical transmembrane domain residues 230-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRLR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16471

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1233D HNHA
1332D 1H-15N HSQC
1412D 1H-15N HSQC
1522D 1H-15N HSQC
1613D HNCO
1713D HN(CA)CB
1813D CBCA(CO)NH
1923D 1H-15N NOESY
11022D 1H-13C HSQC aliphatic
11122D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-13C; U-15N] PRLRTMD, 2 mM DSS, 0.05 % sodium azide, 560 mM DHPC, 20 mM sodium phosphate, 4 mM TCEP, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] PRLRTMD, 2 mM DSS, 0.05 % sodium azide, 700 mM [U-2H] DHPC, 20 mM sodium phosphate, 4 mM TCEP, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-15N] PRLRTMD, 2 mM DSS, 0.05 % sodium azide, 490 mM DHPC, 20 mM sodium phosphate, 4 mM TCEP, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMPRLRTMD-1[U-13C; U-15N]1
2 mMDSS-21
0.05 %sodium azide-31
560 mMDHPC-41
20 mMsodium phosphate-51
4 mMTCEP-61
50 mMsodium chloride-71
1 mMPRLRTMD-8[U-13C; U-15N]2
2 mMDSS-92
0.05 %sodium azide-102
700 mMDHPC-11[U-2H]2
20 mMsodium phosphate-122
4 mMTCEP-132
50 mMsodium chloride-142
0.7 mMPRLRTMD-15[U-15N]3
2 mMDSS-163
0.05 %sodium azide-173
490 mMDHPC-183
20 mMsodium phosphate-193
4 mMTCEP-203
50 mMsodium chloride-213
Sample conditionsIonic strength: 50 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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