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- PDB-3ncb: A mutant human Prolactin receptor antagonist H180A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3ncb
TitleA mutant human Prolactin receptor antagonist H180A in complex with the extracellular domain 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 / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / steroid biosynthetic process / activation of Janus kinase activity ...prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / regulation of epithelial cell differentiation / prolactin signaling pathway / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / steroid biosynthetic process / activation of Janus kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of endothelial cell proliferation / cytokine binding / Prolactin receptor signaling / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / mammary gland alveolus development / regulation of cell adhesion / positive regulation of B cell proliferation / Growth hormone receptor signaling / embryo implantation / positive regulation of protein autophosphorylation / lactation / negative regulation of angiogenesis / response to nutrient levels / female pregnancy / endosome lumen / response to bacterium / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / receptor complex / Amyloid fiber formation / 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/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 ...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
CARBONATE ION / Prolactin / Prolactin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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

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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
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-49 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.210, 124.210, 71.556
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: 21724.814 Da / Num. of mol.: 1 / Fragment: sequence database residues 43-227 / Mutation: H180A, 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: 24445.840 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 26-234
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, 326 molecules

#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: 1.95→33 Å / Num. obs: 46104 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.95-2.028.90.64498.2
2.02-2.1110.453100
2.1-2.2110.328100
2.2-2.3111.10.244100
2.31-2.4611.20.188100
2.46-2.6511.30.135100
2.65-2.9111.30.103100
2.91-3.3311.20.078100
3.33-4.210.80.072100
4.2-3310.30.05699.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.58 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.05 Å
Translation2.5 Å31.05 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: 2.1→32.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 3.87 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 1861 5.1 %RANDOM
Rwork0.18553 ---
obs0.1881 34904 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.686 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-1.06 Å20 Å2
2---2.12 Å20 Å2
3---3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 8 321 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223390
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.9544628
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00624.121165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4915592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7671520
X-RAY DIFFRACTIONr_chiral_restr0.1640.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212620
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_it1.5221.52014
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.71723289
X-RAY DIFFRACTIONr_scbond_it3.89631376
X-RAY DIFFRACTIONr_scangle_it6.1394.51325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 134 -
Rwork0.205 2562 -
obs--100 %

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