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- PDB-2aew: A model for growth hormone receptor activation based on subunit r... -

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Basic information

Entry
Database: PDB / ID: 2aew
TitleA model for growth hormone receptor activation based on subunit rotation within a receptor dimer
ComponentsGrowth hormone receptor
KeywordsHORMONE/GROWTH FACTOR / HORMONE-GROWTH FACTOR complex
Function / homology
Function and homology information


growth hormone receptor activity / regulation of response to nutrient levels / growth hormone receptor complex / taurine metabolic process / response to gravity / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / hormone metabolic process / proline-rich region binding / response to food ...growth hormone receptor activity / regulation of response to nutrient levels / growth hormone receptor complex / taurine metabolic process / response to gravity / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / hormone metabolic process / proline-rich region binding / response to food / growth hormone receptor signaling pathway / response to cycloheximide / cytokine binding / Prolactin receptor signaling / growth factor binding / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / regulation of multicellular organism growth / Growth hormone receptor signaling / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to hormone stimulus / hormone-mediated signaling pathway / SH2 domain binding / response to interleukin-1 / insulin-like growth factor receptor signaling pathway / positive regulation of cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of MAP kinase 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 / receptor complex / external side of plasma membrane / neuronal cell body / lipid binding / protein kinase binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Growth hormone-binding protein / Growth hormone receptor binding / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Growth hormone-binding protein / Growth hormone receptor binding / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Growth hormone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAdams, J.J. / McKinstry, W.J. / Parker, M.W. / Waters, M.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Model for growth hormone receptor activation based on subunit rotation within a receptor dimer.
Authors: Brown, R.J. / Adams, J.J. / Pelekanos, R.A. / Wan, Y. / McKinstry, W.J. / Palethorpe, K. / Seeber, R.M. / Monks, T.A. / Eidne, K.A. / Parker, M.W. / Waters, M.J.
History
DepositionJul 24, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth hormone receptor
B: Growth hormone receptor


Theoretical massNumber of molelcules
Total (without water)47,9022
Polymers47,9022
Non-polymers00
Water66737
1
A: Growth hormone receptor


Theoretical massNumber of molelcules
Total (without water)23,9511
Polymers23,9511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Growth hormone receptor


Theoretical massNumber of molelcules
Total (without water)23,9511
Polymers23,9511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.720, 112.167, 93.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Growth hormone receptor /


Mass: 23950.900 Da / Num. of mol.: 2 / Fragment: residues 29-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10912
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.717882 Å3/Da / Density % sol: 54.744179 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.99 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2003
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionNumber: 14626 / Rmerge(I) obs: 0.082 / Χ2: 1.034 / D res high: 2.7 Å / D res low: 20 Å / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.772099.710.0511.025
4.65.7799.910.0521.014
4.034.610010.0581.042
3.664.0310010.0751.043
3.43.6610010.0851.068
3.23.410010.1061.04
3.043.210010.1491.035
2.913.0410010.2231.038
2.82.9199.910.291.01
2.72.897.810.3241.011
ReflectionResolution: 2.7→20 Å / Num. obs: 14626 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 70 % / Biso Wilson estimate: 53.9 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.034 / Net I/σ(I): 28
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 97.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2 / Num. measured obs: 1421 / Num. unique all: 1421 / Χ2: 1.011 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GHR

1ghr


Resolution: 2.7→14.98 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2149056 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 721 5 %RANDOM
Rwork0.257 ---
all0.262 14626 --
obs0.262 14626 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.499 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å20 Å2
2---13.08 Å20 Å2
3---9.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 0 37 3027
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it2.341.5
X-RAY DIFFRACTIONc_mcangle_it3.92
X-RAY DIFFRACTIONc_scbond_it4.912
X-RAY DIFFRACTIONc_scangle_it6.482.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 110 4.7 %
Rwork0.34 2220 -
all-2330 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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