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- PDB-3npz: Prolactin Receptor (PRLR) Complexed with the Natural Hormone (PRL) -

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Basic information

Entry
Database: PDB / ID: 3npz
TitleProlactin Receptor (PRLR) Complexed with the Natural Hormone (PRL)
Components
  • Prolactin
  • Prolactin receptor
KeywordsHORMONE/HORMONE RECEPTOR / protein protein complex / HORMONE-RECEPTOR complex / HORMONE / HORMONE-HORMONE RECEPTOR complex
Function / homology
Function and homology information


Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / Growth hormone receptor signaling / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelium development / mammary gland epithelial cell differentiation ...Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / Growth hormone receptor signaling / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelium development / mammary gland epithelial cell differentiation / mammary gland development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of endothelial cell proliferation / 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 / positive regulation of protein autophosphorylation / lactation / negative regulation of angiogenesis / response to nutrient levels / female pregnancy / endosome lumen / response to bacterium / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / receptor complex / Amyloid fiber formation / external side of plasma membrane / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / cell surface / extracellular space / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Growth Hormone; Chain: A; - #10 ...Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / 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 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Prolactin / Prolactin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsVan Agthoven, J. / England, P. / Goffin, V. / Broutin, I.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural characterization of the stem-stem dimerization interface between prolactin receptor chains complexed with the natural hormone.
Authors: van Agthoven, J. / Zhang, C. / Tallet, E. / Raynal, B. / Hoos, S. / Baron, B. / England, P. / Goffin, V. / Broutin, I.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolactin
B: Prolactin receptor
C: Prolactin receptor


Theoretical massNumber of molelcules
Total (without water)74,7333
Polymers74,7333
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-23 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.174, 92.174, 216.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Prolactin / PRL


Mass: 22929.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_36753, PRL, RP3-404K8.1-001 / Plasmid: pT7L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01236
#2: Protein Prolactin receptor / / PRL-R / Lactogen receptor


Mass: 25901.920 Da / Num. of mol.: 2 / Fragment: PRLR (unp residues 20-229)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prlr / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05710

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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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium Citrate 100 mM, 14 % PEG 4000, 100 mM LiSO4, 12 % glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.35→84.82 Å / Num. obs: 13695 / % possible obs: 97.8 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 22.7
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1938 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3EW3

3ew3


Resolution: 3.35→84.782 Å / SU ML: 0.44 / σ(F): 1.38 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 683 4.99 %random
Rwork0.2336 ---
obs0.2366 13675 96.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.035 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.1135 Å20 Å2-0 Å2
2--11.1135 Å20 Å2
3----22.2269 Å2
Refinement stepCycle: LAST / Resolution: 3.35→84.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 0 0 4817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014967
X-RAY DIFFRACTIONf_angle_d1.3186740
X-RAY DIFFRACTIONf_dihedral_angle_d19.0181803
X-RAY DIFFRACTIONf_chiral_restr0.081712
X-RAY DIFFRACTIONf_plane_restr0.006852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3501-3.60870.2891470.26142508X-RAY DIFFRACTION97
3.6087-3.97190.28851360.23742534X-RAY DIFFRACTION97
3.9719-4.54660.28581100.20352582X-RAY DIFFRACTION97
4.5466-5.72810.24841290.2082626X-RAY DIFFRACTION97
5.7281-84.80910.33311610.25082742X-RAY DIFFRACTION97

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