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- PDB-1f6f: CRYSTAL STRUCTURE OF THE TERNARY COMPLEX BETWEEN OVINE PLACENTAL ... -

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Basic information

Entry
Database: PDB / ID: 1f6f
TitleCRYSTAL STRUCTURE OF THE TERNARY COMPLEX BETWEEN OVINE PLACENTAL LACTOGEN AND THE EXTRACELLULAR DOMAIN OF THE RAT PROLACTIN RECEPTOR
Components
  • PLACENTAL LACTOGEN
  • PROLACTIN RECEPTOR
KeywordsHORMONE/GROWTH FACTOR/HORMONE RECEPTOR / 4-helical bundle / alpha helical bundle / ternary complex / FN III domains / beta sheet domains / cytokine-receptor complex / HORMONE-GROWTH FACTOR-HORMONE RECEPTOR COMPLEX
Function / homology
Function and homology information


Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / Growth hormone receptor signaling / regulation of epithelial cell differentiation / mammary gland epithelium development / prostate gland growth / mammary gland epithelial cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / cytokine binding ...Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / Growth hormone receptor signaling / regulation of epithelial cell differentiation / mammary gland epithelium development / prostate gland growth / mammary gland epithelial cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / cytokine binding / 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 / positive regulation of protein autophosphorylation / lactation / response to bacterium / hormone activity / 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
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 receptor / Chorionic somatomammotropin hormone
Similarity search - Component
Biological speciesOvis aries (sheep)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsElkins, P.A. / Christinger, H.W. / Sandowski, Y. / Sakal, E. / Gertler, A. / De Vos, A.M. / Kossiakoff, A.A.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Ternary complex between placental lactogen and the extracellular domain of the prolactin receptor.
Authors: Elkins, P.A. / Christinger, H.W. / Sandowski, Y. / Sakal, E. / Gertler, A. / de Vos, A.M. / Kossiakoff, A.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization of Ovine Placental Lactogen in a 1:2 Complex with the Extracellular Domain of the Rat Prolactin Receptor
Authors: Christinger, H.W. / Elkins, P.A. / Sandowski, Y. / Sakal, E. / Gertler, A. / Kossiakoff, A.A. / De Vos, A.M.
History
DepositionJun 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLACENTAL LACTOGEN
B: PROLACTIN RECEPTOR
C: PROLACTIN RECEPTOR


Theoretical massNumber of molelcules
Total (without water)71,7713
Polymers71,7713
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-14 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.180, 63.100, 88.430
Angle α, β, γ (deg.)90.00, 118.63, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a complex of the hormone (chain A) bound to 2 copies of the receptor (chains B and C). The copies of the receptor are not related by precise symmetry.

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Components

#1: Protein PLACENTAL LACTOGEN


Mass: 22601.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Plasmid: PET8 / Production host: Escherichia coli (E. coli) / References: UniProt: P16038
#2: Protein PROLACTIN RECEPTOR /


Mass: 24584.494 Da / Num. of mol.: 2
Fragment: EXTRACELLULAR DOMAIN; N-TERMINAL FIBRONECTIN TYPE III DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P05710
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, isopropanol, MPD, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Details: Christinger, H.W., (1998) Acta Crystallogr., Sect.D, 54, 1408.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %PEG40001reservoir
215 %2-propanol1reservoir
31 %MPD1reservoir
40.1 MMES1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 36413 / Num. obs: 33034 / % possible obs: 90.7 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→30 Å / Rmerge(I) obs: 0.13 / Num. unique all: 2537 / % possible all: 70.4
Reflection shell
*PLUS
% possible obs: 70.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 2.3→30 Å / σ(F): 0.01 / Stereochemistry target values: Engh & Huber
Details: Model bias was reduced by adding experimental phase information using cross-crystal averaging from a non-isomorphous mercury derivative.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2043 -random
Rwork0.225 ---
all-36413 --
obs-33034 90.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 0 120 4627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_bond_d0.012

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