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- PDB-3d48: Crystal structure of a prolactin receptor antagonist bound to the... -

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Basic information

Entry
Database: PDB / ID: 3d48
TitleCrystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor
Components
  • Prolactin
  • Prolactin receptor
KeywordsHormone/Hormone Receptor / Cytokine-Cytokine Receptor Complex / Four-helix Bundle / Glycoprotein / Hormone / Lactation / Secreted / Alternative splicing / Membrane / Receptor / Transmembrane / Hormone-Hormone Receptor COMPLEX
Function / homology
Function and homology information


prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / steroid biosynthetic process / activation of Janus kinase activity ...prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / 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 / 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 / embryo implantation / 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 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
CARBONATE ION / Prolactin / Prolactin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSvensson, L.A. / Breinholt, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor
Authors: Svensson, L.A. / Bondensgaard, K. / Norskov-Lauritsen, L. / Christensen, L. / Becker, P. / Andersen, M.D. / Maltesen, M.J. / Rand, K.D. / Breinholt, J.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Prolactin
R: Prolactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7186
Polymers46,4782
Non-polymers2404
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-4 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.350, 125.350, 69.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Prolactin / PRL


Mass: 21948.000 Da / Num. of mol.: 1 / Fragment: residues 12-199 / Mutation: Q12S, G129R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRL / Plasmid: pET32-a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01236
#2: Protein Prolactin receptor / / PRL-R


Mass: 24529.850 Da / Num. of mol.: 1 / Fragment: Extracellular Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRLR / Plasmid: pET39-b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P16471
#3: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.5M Sodium Chloride, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2007
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 21763 / Num. obs: 21797 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 46.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 22.46
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 21797 / Rsym value: 0.501 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.4.0066refinement
PDB_EXTRACT2data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FOR THE R CHAIN, PDB ENTRY 1BP3. FOR THE P CHAIN, A CORE OF A MODELER HOMOLOGY MODEL BASED ON PDB ENTRIES 1BP3, 1F6F, 1RW5 AND 1N9D.

1bp3

1bp3

1f6f

1rw5

1n9d
PDB Unreleased entry


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.29 / WRfactor Rwork: 0.212 / SU B: 9.77 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1088 5 %RANDOM
Rwork0.218 ---
all0.221 21717 --
obs0.221 20629 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.307 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å2-1.24 Å20 Å2
2---2.48 Å20 Å2
3---3.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2945 0 16 103 3064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223040
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9534121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.695353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91223.885139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.24415522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3941516
X-RAY DIFFRACTIONr_chiral_restr0.1330.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212281
X-RAY DIFFRACTIONr_mcbond_it0.9641.51813
X-RAY DIFFRACTIONr_mcangle_it1.78222929
X-RAY DIFFRACTIONr_scbond_it2.46531227
X-RAY DIFFRACTIONr_scangle_it4.0354.51192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5640.382790.25715011580100
2.564-2.6330.285760.21914411517100
2.633-2.7080.373760.271442151999.934
2.708-2.790.333730.2491380145699.794
2.79-2.8790.321700.2613281398100
2.879-2.9780.359680.23312991367100
2.978-3.0880.311660.2451249131999.697
3.088-3.2110.32650.2531218128599.844
3.211-3.350.323610.221155122099.672
3.35-3.5080.275580.2011116117799.745
3.508-3.6920.264560.20410591115100
3.692-3.9070.252530.2071004106099.717
3.907-4.1660.299500.21938988100
4.166-4.4830.284470.19489694499.894
4.483-4.8870.236430.193811854100
4.887-5.4230.292400.191760800100
5.423-6.1870.303350.218666701100
6.187-7.4020.329310.208585616100
7.402-9.8180.217250.18246949599.798
9.818-200.29160.24231233597.91

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