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- PDB-3ncc: A human Prolactin receptor antagonist in complex with the mutant ... -

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Basic information

Entry
Database: PDB / ID: 3ncc
TitleA human Prolactin receptor antagonist in complex with the mutant extracellular domain H188A of the human prolactin receptor
Components
  • Prolactin
  • Prolactin receptor
KeywordsHORMONE/HORMONE RECEPTOR / pH dependence / hematopoietic cytokine / HORMONE-HORMONE RECEPTOR complex
Function / homology
Function and homology information


prolactin receptor activity / prolactin receptor binding / activation of transmembrane receptor protein tyrosine kinase activity / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / mammary gland epithelial cell differentiation / activation of Janus kinase activity / steroid biosynthetic process / prostate gland growth ...prolactin receptor activity / prolactin receptor binding / activation of transmembrane receptor protein tyrosine kinase activity / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / mammary gland epithelial cell differentiation / activation of Janus kinase activity / steroid biosynthetic process / prostate gland growth / cellular response to granulocyte macrophage colony-stimulating factor stimulus / mammary gland development / Prolactin receptor signaling / cytokine binding / negative regulation of endothelial cell proliferation / peptide hormone binding / mammary gland alveolus development / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / regulation of cell adhesion / lactation / positive regulation of B cell proliferation / embryo implantation / negative regulation of angiogenesis / endosome lumen / positive regulation of receptor signaling pathway via JAK-STAT / response to bacterium / response to nutrient levels / female pregnancy / hormone activity / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / receptor complex / Amyloid fiber formation / external side of plasma membrane / positive regulation of cell population proliferation / lipid binding / protein kinase binding / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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. / : ...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 3 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
CARBONATE ION / Prolactin / Prolactin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKulkarni, M.V. / Tettamanzi, M.C. / Murphy, J.W. / Keeler, C. / Myszka, D.G. / Chayen, N.E. / Lolis, E.J. / Hodsdon, M.E.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation.
Authors: Kulkarni, M.V. / Tettamanzi, M.C. / Murphy, J.W. / Keeler, C. / Myszka, D.G. / Chayen, N.E. / Lolis, E.J. / Hodsdon, M.E.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 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: Prolactin
B: Prolactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3357
Polymers46,1712
Non-polymers1645
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-49 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.411, 123.411, 73.148
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Prolactin / PRL


Mass: 21791.883 Da / Num. of mol.: 1 / Fragment: sequence database residues 43-227 / Mutation: G129R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hPRL, PRL / Plasmid: pT7L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01236
#2: Protein Prolactin receptor / PRL-R


Mass: 24378.771 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 26-234 / Mutation: H188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hPRLr, PRLR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16471

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Non-polymers , 4 types, 234 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.7M NaCl, 0.1 M Hepes 7.5, 6% PEG monomethylether 550, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.25→33 Å / Num. obs: 30305 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.25-2.3310.80.815100
2.33-2.4211.20.695100
2.42-2.5311.20.519100
2.53-2.6711.30.381100
2.67-2.8311.30.274100
2.83-3.0511.30.191100
3.05-3.3611.30.118100
3.36-3.8511.20.092100
3.85-4.8411.10.075100
4.84-33110.06100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.03 Å
Translation2.5 Å32.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MZG

3mzg


Resolution: 2.5→32.03 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 7.314 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1114 5 %RANDOM
Rwork0.17768 ---
obs0.18082 20987 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.988 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å2-1.36 Å20 Å2
2---2.71 Å20 Å2
3---4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 8 229 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9554538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.275400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23524.025159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70415578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5661519
X-RAY DIFFRACTIONr_chiral_restr0.1270.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212555
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2061.51987
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33323233
X-RAY DIFFRACTIONr_scbond_it3.35531346
X-RAY DIFFRACTIONr_scangle_it5.5964.51298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 76 -
Rwork0.23 1544 -
obs--100 %

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