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- PDB-2lfg: Solution structure of the human prolactin receptor ecd domain d2 -

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Basic information

Entry
Database: PDB / ID: 2lfg
TitleSolution structure of the human prolactin receptor ecd domain d2
ComponentsProlactin receptor
KeywordsHORMONE RECEPTOR / Extracellular domain / Cytokine 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 / cytokine binding / Prolactin receptor signaling ...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 / cytokine binding / Prolactin receptor signaling / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / mammary gland alveolus development / regulation of cell adhesion / positive regulation of B cell proliferation / Growth hormone receptor signaling / embryo implantation / positive regulation of protein autophosphorylation / lactation / 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 / Immunoglobulins / Immunoglobulin-like fold ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsDagil, R. / Knudsen, M.J. / Kragelund, B.B. / O'Shea, C. / Teilum, K.
CitationJournal: Structure / Year: 2012
Title: The WSXWS Motif in Cytokine Receptors Is a Molecular Switch Involved in Receptor Activation: Insight from Structures of the Prolactin Receptor
Authors: Dagil, R. / Knudsen, M.J. / Olsen, J.G. / O'Shea, C. / Franzmann, M. / Goffin, V. / Teilum, K. / Breinholt, J. / Kragelund, B.B.
History
DepositionJun 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: 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_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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)13,3431
Polymers13,3431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100
RepresentativeModel #1lowest energy

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Components

#1: Protein Prolactin receptor / / PRL-R


Mass: 13343.341 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III 2 domain residues 99-210
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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1913D CBCA(CO)NH
11013D HN(CA)CO
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11313D (H)CCH-TOCSY
11413D 1H-13C NOESY aliphatic
11513D 1H-13C NOESY aromatic
11622D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] protein, 10 mM sodium phosphate, 10 mM TCEP, 1 mM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C(1)] protein, 10 mM sodium phosphate, 10 mM TCEP, 0.02 % sodium azide, 1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate-21
10 mMTCEP-31
1 mMDSS-41
0.02 %sodium azide-51
0.5 mMprotein-6[U-100% 13C(1)]2
10 mMsodium phosphate-72
10 mMTCEP-82
0.02 %sodium azide-92
1 mMDSS-102
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA2.2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPN2.1.5CCPNpeak picking
ARIA2.3.2Linge, O'Donoghue and Nilgeswater refinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1562 / NOE intraresidue total count: 345 / NOE long range total count: 583 / NOE medium range total count: 634 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 55
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.25 Å / Maximum upper distance constraint violation: 0.34 Å

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