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- PDB-1hwg: 1:2 COMPLEX OF HUMAN GROWTH HORMONE WITH ITS SOLUBLE BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1hwg
Title1:2 COMPLEX OF HUMAN GROWTH HORMONE WITH ITS SOLUBLE BINDING PROTEIN
Components
  • GROWTH HORMONE
  • GROWTH HORMONE BINDING PROTEIN
KeywordsCOMPLEX (HORMONE/RECEPTOR) / CYTOKINE / HORMONE / RECEPTOR / HEMATOPOIETIC / COMPLEX (HORMONE-RECEPTOR) / COMPLEX (HORMONE-RECEPTOR) complex
Function / homology
Function and homology information


regulation of response to nutrient levels / growth hormone receptor activity / growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / taurine metabolic process / animal organ development / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth ...regulation of response to nutrient levels / growth hormone receptor activity / growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / taurine metabolic process / animal organ development / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / positive regulation of D-glucose transmembrane transport / proline-rich region binding / hormone metabolic process / cell surface receptor signaling pathway via STAT / growth hormone receptor binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor signaling pathway / response to food / growth factor binding / response to cycloheximide / Prolactin receptor signaling / response to gravity / cytokine binding / positive regulation of MAP kinase activity / peptide hormone binding / regulation of multicellular organism growth / growth hormone receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / cellular response to hormone stimulus / hormone-mediated signaling pathway / SH2 domain binding / insulin-like growth factor receptor signaling pathway / response to interleukin-1 / response to glucocorticoid / endosome lumen / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of cell differentiation / growth factor activity / response to nutrient levels / hormone activity / receptor internalization / cytoplasmic ribonucleoprotein granule / endocytosis / cellular response to insulin stimulus / cytokine-mediated signaling pathway / 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 / positive regulation of cell population proliferation / lipid binding / protein kinase binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / metal ion binding / identical protein binding / membrane / 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 / Growth hormone/erythropoietin receptor, ligand binding ...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 / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSundstrom, S.M. / Lundqvist, T.
CitationJournal: J.Biol.Chem. / Year: 1996
Title: Crystal structure of an antagonist mutant of human growth hormone, G120R, in complex with its receptor at 2.9 A resolution.
Authors: Sundstrom, M. / Lundqvist, T. / Rodin, J. / Giebel, L.B. / Milligan, D. / Norstedt, G.
History
DepositionNov 13, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROWTH HORMONE
B: GROWTH HORMONE BINDING PROTEIN
C: GROWTH HORMONE BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)76,7153
Polymers76,7153
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-22 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.610, 69.020, 76.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GROWTH HORMONE


Mass: 22151.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01241
#2: Protein GROWTH HORMONE BINDING PROTEIN


Mass: 27281.641 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Details: ONE HORMONE WITH TWO RECEPTOR MOLECULES / 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.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: THE PROTEIN COMPLEX WAS CRYSTALLISED AT PH 6.5 USING 45% (W/V) LISO4 WITH 2% PEG-500 DME AND SOAKED TO PH 5.5 PRIOR TO DATA COLLECTION
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.25 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
146 %(v/v)sat1reservoirLiSO4
22 %PEG5001reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1994
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 25222 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rsym value: 0.097 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.313 / % possible all: 81.2
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Rmerge(I) obs: 0.313

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HHR

2hhr
PDB Unreleased entry


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1261 5 %RANDOM
Rwork0.199 ---
obs0.199 25222 94.3 %-
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 0 175 919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.53
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
LS refinement shellResolution: 2.5→2.7 Å / Total num. of bins used: 6 / % reflection obs: 81.2 %

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