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- PDB-1a22: HUMAN GROWTH HORMONE BOUND TO SINGLE RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1a22
TitleHUMAN GROWTH HORMONE BOUND TO SINGLE RECEPTOR
Components
  • GROWTH HORMONE
  • GROWTH HORMONE RECEPTOR
KeywordsCOMPLEX (HORMONE/RECEPTOR) / COMPLEX (HORMONE-RECEPTOR) / PITUITARY / HORMONE / 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 / bone maturation / prolactin receptor binding / taurine metabolic process / animal organ development / response to gravity / cartilage development involved in endochondral bone morphogenesis ...regulation of response to nutrient levels / growth hormone receptor activity / growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / taurine metabolic process / animal organ development / response to gravity / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / growth hormone receptor binding / positive regulation of D-glucose transmembrane transport / proline-rich region binding / cell surface receptor signaling pathway via STAT / hormone metabolic process / positive regulation of insulin-like growth factor receptor signaling pathway / response to food / growth hormone receptor signaling pathway / response to cycloheximide / growth factor binding / Prolactin receptor signaling / cytokine binding / peptide hormone binding / growth hormone receptor signaling pathway via JAK-STAT / regulation of multicellular organism growth / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / cellular response to hormone stimulus / response to glucocorticoid / hormone-mediated signaling pathway / positive regulation of MAP kinase activity / response to interleukin-1 / SH2 domain binding / insulin-like growth factor receptor signaling pathway / cytokine activity / endosome lumen / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of cell differentiation / growth factor activity / response to nutrient levels / cytokine-mediated signaling pathway / hormone activity / receptor internalization / cytoplasmic ribonucleoprotein granule / cellular response to insulin stimulus / endocytosis / 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 / 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 / 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: 2.6 Å
AuthorsDe Vos, A.M. / Ultsch, M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity.
Authors: Clackson, T. / Ultsch, M.H. / Wells, J.A. / de Vos, A.M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystals of Human Growth Hormone-Receptor Complexes. Extracellular Domains of the Growth Hormone and Prolactin Receptors and a Hormone Mutant Designed to Prevent Receptor Dimerization
Authors: Ultsch, M. / De Vos, A.M.
History
DepositionJan 15, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 23, 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 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)49,6622
Polymers49,6622
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-7 kcal/mol
Surface area17780 Å2
MethodPISA
2
A: GROWTH HORMONE
B: GROWTH HORMONE RECEPTOR

A: GROWTH HORMONE
B: GROWTH HORMONE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)99,3244
Polymers99,3244
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7630 Å2
ΔGint-23 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.700, 67.700, 228.000
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 GROWTH HORMONE


Mass: 22252.135 Da / Num. of mol.: 1 / Mutation: G120R
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 RECEPTOR


Mass: 27409.771 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
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.: 69 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Ultsch, M., (1993) J.Mol.Biol., 231, 1133.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %satammonium sulfate1reservoir
2120 mM1dropNaCl
320 mMsodium acetate1drop
41 mMPMSF1drop
50.1 MBis-Tris1drop
610 %satammonium sulfate1drop
71 %(v/v)MPD1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1991
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. obs: 14489 / % possible obs: 85 % / Redundancy: 4 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 7.1 / % possible all: 78
Reflection
*PLUS
Num. measured all: 51354
Reflection shell
*PLUS
% possible obs: 78 % / Num. unique obs: 1552 / Num. measured obs: 3934

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HHR

3hhr


Resolution: 2.6→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1 / Isotropic thermal model: INDIVIDUAL RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.187 --
obs0.187 13872 85 %
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 0 0 69 3113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.6
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_it2.1
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it2.8
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 8 /
Num. reflection% reflection
Rwork1600 -
obs-78 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.281

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