[English] 日本語
Yorodumi
- PDB-3ew3: the 1:2 complex between a Nterminal elongated prolactin and the e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ew3
Titlethe 1:2 complex between a Nterminal elongated prolactin and the extra cellular domain of the rat prolactin receptor
Components
  • Prolactin
  • Prolactin receptor
KeywordsHORMONE/HORMONE RECEPTOR / complex / Glycoprotein / Hormone / Lactation / Secreted / Alternative splicing / Membrane / Receptor / Transmembrane / HORMONE-HORMONE RECEPTOR COMPLEX
Function / homology
Function and homology information


Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / Growth hormone receptor signaling / regulation of epithelial cell differentiation / prolactin signaling pathway / mammary gland epithelium development / prostate gland growth / mammary gland epithelial cell differentiation ...Prolactin receptor signaling / prolactin receptor activity / prolactin receptor binding / positive regulation of lactation / Growth hormone receptor signaling / regulation of epithelial cell differentiation / prolactin signaling pathway / mammary gland epithelium development / prostate gland growth / mammary gland epithelial cell differentiation / mammary gland development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / Prolactin receptor signaling / cytokine binding / negative regulation of endothelial cell proliferation / peptide hormone binding / cell surface receptor signaling pathway via JAK-STAT / mammary gland alveolus development / regulation of cell adhesion / Growth hormone receptor signaling / positive regulation of B cell proliferation / positive regulation of protein autophosphorylation / lactation / negative regulation of angiogenesis / response to nutrient levels / endosome lumen / female pregnancy / response to bacterium / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / cytokine-mediated signaling pathway / positive regulation of miRNA transcription / 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 III domain / 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
Prolactin / Prolactin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsBroutin, I. / Jomain, J.B. / England, P. / Goffin, V.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2.
Authors: Broutin, I. / Jomain, J.B. / Tallet, E. / van Agthoven, J. / Raynal, B. / Hoos, S. / Kragelund, B.B. / Kelly, P.A. / Ducruix, A. / England, P. / Goffin, V.
History
DepositionOct 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prolactin
B: Prolactin receptor
C: Prolactin receptor


Theoretical massNumber of molelcules
Total (without water)75,6803
Polymers75,6803
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-17 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.120, 92.120, 215.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Prolactin / PRL


Mass: 23613.959 Da / Num. of mol.: 1 / Fragment: UNP residues 43-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRL / Plasmid: PQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01236
#2: Protein Prolactin receptor / PRL-R / Lactogen receptor


Mass: 26033.115 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prlr / Plasmid: pRc/CMV / Production host: Escherichia coli (E. coli) / Strain (production host): M15-rep4 / References: UniProt: P05710
Sequence detailsFIRST 14 AA REPLACED BY N-TERMINUS 17 AA FROM OPL: P16038 CSH_SHEEP

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.34 % / Mosaicity: 1.053 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM LiSO4, 100mM NaCitrate pH 5.6, 12% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2006 / Details: mirror
RadiationMonochromator: torodial focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.5→107.833 Å / Num. obs: 10464 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6.536
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.7-3.95.20.1763.9763914830.17699.9
3.9-4.145.10.1534.5734514340.153100
4.14-4.425.10.1086682613420.10899.8
4.42-4.7850.0926.8622912350.09299.8
4.78-5.2350.0798.1575811600.07999.4
5.23-5.854.90.0946.6519810620.09499.2
5.85-6.764.70.0986.344049300.09898.9
6.76-8.274.40.0738.435077950.07397.2
8.27-11.74.50.05710.828596390.05798
11.7-107.833.50.0679.513613840.06794.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å62.36 Å
Translation4 Å62.36 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F6F

1f6f


Resolution: 3.8→14.997 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.684 / SU ML: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.41 / σ(I): 0 / Phase error: 35.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3237 502 5.32 %RANDOM
Rwork0.2521 ---
obs0.256 9437 98.69 %-
all-10464 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 41.849 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso max: 78.74 Å2 / Biso mean: 43.14 Å2 / Biso min: 12.99 Å2
Baniso -1Baniso -2Baniso -3
1-18.3457 Å20 Å20 Å2
2--18.3457 Å20 Å2
3----36.6914 Å2
Refinement stepCycle: LAST / Resolution: 3.8→14.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 0 0 4694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094843
X-RAY DIFFRACTIONf_angle_d1.2476573
X-RAY DIFFRACTIONf_dihedral_angle_d23.0931770
X-RAY DIFFRACTIONf_chiral_restr0.085691
X-RAY DIFFRACTIONf_plane_restr0.006833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.8001-4.1750.40311260.30712206100
4.175-4.76210.31281170.24892204100
4.7621-5.93720.31191300.2336223499
5.9372-14.99760.28831290.2287229197
Xplor fileSerial no: 1 / Param file: protein_rep.param

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more