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- PDB-5ohd: Putative inactive (dormant) dimeric state of GHR transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 5ohd
TitlePutative inactive (dormant) dimeric state of GHR transmembrane domain
ComponentsGrowth hormone receptor
KeywordsMEMBRANE PROTEIN / Dimer / GHR / Growth hormone receptor / Homodimer / Human / Receptor / Transmembrane domain / JAK2 tyrosine kinase
Function / homology
Function and homology information


regulation of response to nutrient levels / growth hormone receptor activity / growth hormone receptor complex / taurine metabolic process / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / proline-rich region binding / hormone metabolic process / growth hormone receptor signaling pathway / response to food ...regulation of response to nutrient levels / growth hormone receptor activity / growth hormone receptor complex / taurine metabolic process / cartilage development involved in endochondral bone morphogenesis / positive regulation of multicellular organism growth / proline-rich region binding / hormone metabolic process / 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 / 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 / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of cell differentiation / receptor internalization / cytoplasmic ribonucleoprotein granule / endocytosis / cellular response to insulin stimulus / cytokine-mediated signaling pathway / response to estradiol / protein phosphatase binding / 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 / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Growth hormone-binding protein / Growth hormone receptor binding / Long hematopoietin receptor, single chain, conserved site / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Long hematopoietin receptor, single chain family signature. / Fibronectin type III domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Growth hormone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLesovoy, D.M. / Bocharov, E.V. / Bocharova, O.V. / Urban, A.S. / Arseniev, A.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-50-00131 Russian Federation
Citation
Journal: Biochim. Biophys. Acta / Year: 2018
Title: Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor.
Authors: Bocharov, E.V. / Lesovoy, D.M. / Bocharova, O.V. / Urban, A.S. / Pavlov, K.V. / Volynsky, P.E. / Efremov, R.G. / Arseniev, A.S.
#1: Journal: Bioorg. Khim. / Year: 2015
Title: Preparation of Transmembrane Fragments Growth Hormone Receptor GHR in a Cell-Free Expression System for Structural Studies.
Authors: Bocharova, O.V. / Kuzmichev, P.K. / Urban, A.S. / Goncharuk, S.A. / Bocharov, E.V. / Arsenyev, A.S.
History
DepositionJul 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jul 3, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,2902
Polymers10,2902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area890 Å2
ΔGint-14 kcal/mol
Surface area9540 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Growth hormone receptor / GH receptor / Somatotropin receptor


Mass: 5145.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The author sequence numbering corresponds to the Swiss-Prot annotation of the human Growth hormone receptor (GHR), P10912
Source: (gene. exp.) Homo sapiens (human) / Gene: GHR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10912

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic215N,13C-F1-filtered/F3-edited-NOESY
123isotropic215N,13C-F1-filtered/F3-edited-NOESY
133isotropic13D 1H-13C(constant time) NOESY aliphatic
143isotropic23D 1H-13C NOESY aliphatic
152isotropic13D 1H-15N(TROSY) NOESY
163isotropic13D 1H-13C NOESY aromatic
172isotropic13D 1H-15N(TROSY) HNHB
182isotropic13D 1H-15N(TROSY) HNHA
193isotropic13D 1H-15N(TROSY) HNCO
1103isotropic13D 1H-15N(TROSY) HNCA
1113isotropic13D 1H-15N(TROSY) HN(CA)CO
1123isotropic13D 1H-15N(TROSY) HN(CO)CA
1131isotropic12D 1H-15N HSQC
1141isotropic12D 1H-15N TROSY
1153isotropic12D 1H-INEPT-13CA-detected
1161isotropic12D 1H-13C constant time HSQC aliphatic
1171isotropic12D 1H-13C constant time HSQC aromatic
1183isotropic12D 1H-13C(TROSY) constant time HSQC aromatic
1193isotropic23D (H)CCH-TOCSY
1203isotropic13D 1H-13C constant time (H)CCH-TOCSY
1212isotropic12D 1H-15N CSA/dipole cross-correlation
1222isotropic12D 1H-15N(TROSY) CLEANEX

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle10.7 mM [U-99% 13C; U-99% 15N] GHRtm, 1.2 mM GHRtm, 100 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2Ofor intermolecular NOEsample_195% H2O/5% D2O
micelle20.8 mM [U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2Osample_295% H2O/5% D2O
micelle30.8 mM [U-99% 13C; U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2Oreference for intermolecular NOEsample_395% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMGHRtm-13C-15N[U-99% 13C; U-99% 15N]1
1.2 mMGHRtmnatural abundance1
100 mMDPC[U-99% 2H]1
0.3 mMsodium azidenatural abundance1
8 mMTCEPnatural abundance1
10 mMcitric acidnatural abundance1
20 mMNa2HPO4natural abundance1
0.8 mMGHRtm[U-99% 15N]2
50 mMDPC[U-99% 2H]2
0.3 mMsodium azidenatural abundance2
8 mMTCEPnatural abundance2
10 mMcitric acidnatural abundance2
20 mMNa2HPO4natural abundance2
0.8 mMGHRtm[U-99% 13C; U-99% 15N]3
50 mMDPC[U-99% 2H]3
0.3 mMsodium azidenatural abundance3
8 mMTCEPnatural abundance3
10 mMcitric acidnatural abundance3
20 mMNa2HPO4natural abundance3
Sample conditionsIonic strength: 40 mM / Ionic strength err: 10 / Label: sample_conditions_1 / pH: 5 / PH err: 0.05 / Pressure: AMBIENT atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III800113C 1H CryoProbe
Bruker AVANCE IIIBrukerAVANCE III60021H CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CARA1.9Keller and Wuthrichchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
MathematicaLinuxWolfram Researchdata analysis
MddNMR2.4V. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczukprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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