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- PDB-1kf9: PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1kf9
TitlePHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR
Components
  • EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
  • PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
KeywordsHORMONE/GROWTH FACTOR / CYTOKINE / HORMONE-RECEPTOR COMPLEX / PHAGE DISPLAY MOLECULAR PLASTICITY / RECEPTOR HOMODIMERIZATION / HUMAN GROWTH HORMONE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


growth hormone receptor activity / regulation of response to nutrient levels / growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / positive regulation of growth / taurine metabolic process / animal organ development / positive regulation of activation of Janus kinase activity ...growth hormone receptor activity / regulation of response to nutrient levels / growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / positive regulation of growth / taurine metabolic process / animal organ development / positive regulation of activation of Janus kinase activity / response to gravity / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / hormone metabolic process / positive regulation of glucose transmembrane transport / proline-rich region binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor binding / response to food / growth hormone receptor signaling pathway / response to cycloheximide / Prolactin receptor signaling / cytokine binding / growth factor binding / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / regulation of multicellular organism growth / Synthesis, secretion, and deacylation of Ghrelin / Growth hormone receptor signaling / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to hormone stimulus / hormone-mediated signaling pathway / response to interleukin-1 / SH2 domain binding / response to nutrient levels / insulin-like growth factor receptor signaling pathway / cytokine activity / endosome lumen / positive regulation of cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of MAP kinase activity / growth factor activity / hormone activity / receptor internalization / cytokine-mediated signaling pathway / cytoplasmic ribonucleoprotein granule / endocytosis / cellular response to insulin stimulus / positive regulation of peptidyl-tyrosine phosphorylation / response to estradiol / protein phosphatase binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / external side of plasma membrane / neuronal cell body / lipid binding / protein kinase binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Growth hormone-binding protein / Growth hormone receptor binding / Somatotropin / 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-binding protein / Growth hormone receptor binding / Somatotropin / 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-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
Somatotropin / Growth hormone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchiffer, C.A. / Ultsch, M. / Walsh, S. / Somers, W. / De Vos, A.M. / Kossiakoff, A.A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of a Phage Display Derived Variant of Human Growth Hormone Complexed to Two Copies of the Extracellular Domain of its Receptor: Evidence for Strong Structural Coupling between Receptor Binding Sites
Authors: Schiffer, C.A. / Ultsch, M. / Walsh, S. / Somers, W. / De Vos, A.M. / Kossiakoff, A.A.
History
DepositionNov 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE The sequence of the molecules A and D have not been deposited in any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
B: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
C: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
D: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
E: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
F: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Theoretical massNumber of molelcules
Total (without water)153,6126
Polymers153,6126
Non-polymers00
Water1,33374
1
A: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
B: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
C: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Theoretical massNumber of molelcules
Total (without water)76,8063
Polymers76,8063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-18 kcal/mol
Surface area24750 Å2
MethodPISA
2
D: PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
E: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
F: EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Theoretical massNumber of molelcules
Total (without water)76,8063
Polymers76,8063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-19 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.289, 111.937, 95.290
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE


Mass: 21986.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01241*PLUS
#2: Protein
EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)


Mass: 27409.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10912
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growpH: 6.3 / Details: pH 6.30
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium citrate1reservoir
430 %PEG25001reservoirpH6.3

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 43162 / % possible obs: 95.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 215604
Reflection shell
*PLUS
% possible obs: 78.8 %

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Processing

Software
NameVersionClassification
SCALEdata collection
MARSCALEdata reduction
X-PLORmodel building
X-PLOR3.843refinement
SCALEdata reduction
MARSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1798 5 %RANDOM 5%
Rwork0.234 ---
obs0.234 39338 90.5 %-
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20.3 Å2
2---5.9 Å20 Å2
3---14.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8604 0 0 74 8678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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