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- PDB-1bp3: THE XRAY STRUCTURE OF A GROWTH HORMONE-PROLACTIN RECEPTOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bp3
TitleTHE XRAY STRUCTURE OF A GROWTH HORMONE-PROLACTIN RECEPTOR COMPLEX
Components
  • PROTEIN (GROWTH HORMONE)
  • PROTEIN (PROLACTIN RECEPTOR)
KeywordsHORMONE/GROWTH FACTOR / HORMONE / RECEPTOR / HORMONE-GROWTH FACTOR complex
Function / homology
Function and homology information


growth hormone receptor complex / prolactin receptor activity / bone maturation / prolactin receptor binding / positive regulation of growth / animal organ development / regulation of epithelial cell differentiation / positive regulation of activation of Janus kinase activity / prostate gland growth / mammary gland epithelial cell differentiation ...growth hormone receptor complex / prolactin receptor activity / bone maturation / prolactin receptor binding / positive regulation of growth / animal organ development / regulation of epithelial cell differentiation / positive regulation of activation of Janus kinase activity / prostate gland growth / mammary gland epithelial cell differentiation / steroid biosynthetic process / positive regulation of multicellular organism growth / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of glucose transmembrane transport / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor binding / activation of transmembrane receptor protein tyrosine kinase activity / growth hormone receptor signaling pathway / cytokine binding / Prolactin receptor signaling / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / mammary gland alveolus development / regulation of cell adhesion / positive regulation of B cell proliferation / Growth hormone receptor signaling / positive regulation of tyrosine phosphorylation of STAT protein / embryo implantation / positive regulation of protein autophosphorylation / lactation / response to nutrient levels / cytokine activity / endosome lumen / response to bacterium / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of MAP kinase activity / hormone activity / cytokine-mediated signaling pathway / response to estradiol / positive regulation of cold-induced thermogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / external side of plasma membrane / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / cell surface / extracellular space / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Somatotropin / Prolactin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSomers, W. / Ultsch, M. / De Vos, A.M. / Kossiakoff, A.A.
CitationJournal: Nature / Year: 1994
Title: The X-ray structure of a growth hormone-prolactin receptor complex.
Authors: Somers, W. / Ultsch, M. / De Vos, A.M. / Kossiakoff, A.A.
History
DepositionAug 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GROWTH HORMONE)
B: PROTEIN (PROLACTIN RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8613
Polymers46,7962
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.200, 69.800, 43.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 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 PROTEIN (PROLACTIN RECEPTOR)


Mass: 24543.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P16471
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growpH: 6 / Details: pH 6.00

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.908
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.9→10 Å / Num. obs: 9883 / % possible obs: 93 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 2.9→3 Å / % possible all: 89

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A22

1a22


Resolution: 2.9→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.22 --
obs-53033 93 %
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 1 0 3123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d0.046
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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