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- PDB-3hhr: HUMAN GROWTH HORMONE AND EXTRACELLULAR DOMAIN OF ITS RECEPTOR: CR... -

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Basic information

Entry
Database: PDB / ID: 3hhr
TitleHUMAN GROWTH HORMONE AND EXTRACELLULAR DOMAIN OF ITS RECEPTOR: CRYSTAL STRUCTURE OF THE COMPLEX
Components
  • HUMAN GROWTH HORMONE
  • HUMAN GROWTH HORMONE RECEPTOR (hGHbp)
KeywordsHORMONE/RECEPTOR / 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 / response to interleukin-1 / insulin-like growth factor receptor signaling pathway / 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 / Resolution: 2.8 Å
AuthorsDe Vos, A.M. / Ultsch, M. / Kossiakoff, A.A.
Citation
Journal: Science / Year: 1992
Title: Human growth hormone and extracellular domain of its receptor: crystal structure of the complex.
Authors: de Vos, A.M. / Ultsch, M. / Kossiakoff, A.A.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystals of the Complex between Human Growth Hormone and the Extracellular Domain of its Receptor
Authors: Ultsch, M. / De Vos, A.M. / Kossiakoff, A.A.
#2: Journal: Science / Year: 1991
Title: Dimerization of the Extracellular Domain of the Human Growth Hormone Receptor by a Single Hormone Molecule
Authors: Cunningham, B.C. / Ultsch, M. / De Vos, A.M. / Mulkerrin, M.G. / Clauser, K.R. / Wells, J.A.
History
DepositionDec 30, 1993Processing site: BNL
SupersessionApr 30, 1994ID: 2HHR
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: 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: HUMAN GROWTH HORMONE
B: HUMAN GROWTH HORMONE RECEPTOR (hGHbp)
C: HUMAN GROWTH HORMONE RECEPTOR (hGHbp)


Theoretical massNumber of molelcules
Total (without water)70,0133
Polymers70,0133
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-19 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.800, 68.600, 76.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: ASP B 52 - GLU B 53 OMEGA =220.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLU B 53 - VAL B 54 OMEGA =214.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: LEU B 233 - PRO B 234 OMEGA = 31.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLY C 62 - PRO C 63 OMEGA =149.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein HUMAN GROWTH HORMONE


Mass: 22004.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01241
#2: Protein HUMAN GROWTH HORMONE RECEPTOR (hGHbp)


Mass: 24004.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P10912
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 222.865-868
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %(w/v)satammonium sulfate1reservoir
21 %MPD1reservoir
34 mg/mlcomplex1drop
540 %(w/v)satammonium sulfate1drop
61 %MPD1drop
4Tris-HCl1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.204

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.221 / Rfactor obs: 0.221 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 0 0 4614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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