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- PDB-1axi: STRUCTURAL PLASTICITY AT THE HGH:HGHBP INTERFACE -

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Basic information

Entry
Database: PDB / ID: 1axi
TitleSTRUCTURAL PLASTICITY AT THE HGH:HGHBP INTERFACE
Components
  • GROWTH HORMONE
  • GROWTH HORMONE RECEPTOR
KeywordsCOMPLEX (HORMONE/RECEPTOR) / 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 / insulin-like growth factor receptor signaling pathway / SH2 domain binding / response to interleukin-1 / response to glucocorticoid / cytokine activity / endosome lumen / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of cell differentiation / response to nutrient levels / hormone activity / receptor internalization / endocytosis / cellular response to insulin stimulus / cytoplasmic ribonucleoprotein granule / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAtwell, S. / Ultsch, M. / De Vos, A.M. / Wells, J.A.
Citation
Journal: Science / Year: 1997
Title: Structural plasticity in a remodeled protein-protein interface.
Authors: Atwell, S. / Ultsch, M. / De Vos, A.M. / Wells, J.A.
#1: 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.
History
DepositionOct 15, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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: GROWTH HORMONE
B: GROWTH HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3493
Polymers49,2532
Non-polymers961
Water6,882382
1
A: GROWTH HORMONE
B: GROWTH HORMONE RECEPTOR
hetero molecules

A: GROWTH HORMONE
B: GROWTH HORMONE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6996
Polymers98,5074
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8700 Å2
ΔGint-73 kcal/mol
Surface area32580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.600, 65.600, 231.700
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 / HGH


Mass: 22230.113 Da / Num. of mol.: 1 / Mutation: G120R, K168R, D171T, K172Y, E174A, F176Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PB0720 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 34B8 / References: UniProt: P01241
#2: Protein GROWTH HORMONE RECEPTOR / HGHBP


Mass: 27023.260 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR BINDING DOMAIN / Mutation: W104A
Source method: isolated from a genetically manipulated source
Details: HGHBP WITH FUNCTIONALLY CRITICAL TRP 104 MUTATED TO ALA
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PB0720 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 33B6 / References: UniProt: P10912
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 51.37 %
Crystal growMethod: streak seeding / pH: 6.5
Details: CRYSTALLIZED BY STREAK SEEDING AT 5MG/ML COMPLEX IN 50MM BIS-TRIS (PH 6.5) 20% SATURATED AMMONIUM SULFATE, streak seeding
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
250 mMBis-Tris11
317-20 %satammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC / Detector: CCD / Date: May 5, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 28276 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 7.4 / % possible all: 51.3
Reflection
*PLUS
Num. measured all: 133933

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HGH(G120R):HGHBP STRUCTURE (IN PREPARATION)

Resolution: 2.1→7 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2112 8 %RANDOM
Rwork0.19 ---
obs-26402 --
Displacement parameters
Baniso -1Baniso -3
1--4 Å2-
3--8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 5 382 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it2.242.5
X-RAY DIFFRACTIONp_mcangle_it3.173.5
X-RAY DIFFRACTIONp_scbond_it2.922.5
X-RAY DIFFRACTIONp_scangle_it4.273.5
X-RAY DIFFRACTIONp_plane_restr0.030.03
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.20.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor19.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.120
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 26402 / Num. reflection obs: 24290 / Rfactor all: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.7 Å2

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