[English] 日本語
Yorodumi
- PDB-4f8k: Molecular analysis of the interaction between the prostacyclin re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f8k
TitleMolecular analysis of the interaction between the prostacyclin receptor and the first PDZ domain of PDZK1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF3, Prostacyclin receptor
KeywordsSIGNALING PROTEIN / PDZ domain / Adaptor protein / Prostacyclin receptor / Chimera protein / fusion protein
Function / homology
Function and homology information


Prostanoid ligand receptors / prostacyclin receptor activity / Prostacyclin signalling through prostacyclin receptor / G alpha (s) signalling events / scavenger receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / microvillus membrane / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / regulation of monoatomic anion transport ...Prostanoid ligand receptors / prostacyclin receptor activity / Prostacyclin signalling through prostacyclin receptor / G alpha (s) signalling events / scavenger receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / microvillus membrane / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / regulation of monoatomic anion transport / protein localization to plasma membrane / negative regulation of smooth muscle cell proliferation / brush border membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / in utero embryonic development / response to lipopolysaccharide / inflammatory response / apical plasma membrane / signaling receptor binding / protein-containing complex binding / plasma membrane / cytosol
Similarity search - Function
Prostacyclin (prostanoid IP) receptor / : / Prostanoid receptor / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Prostacyclin (prostanoid IP) receptor / : / Prostanoid receptor / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Roll / Mainly Beta
Similarity search - Domain/homology
Prostacyclin receptor / Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKocher, O. / Birrane, G. / Kinsella, B.T. / Mulvaney, E.P.
CitationJournal: Plos One / Year: 2013
Title: Molecular Analysis of the Prostacyclin Receptor's Interaction with the PDZ1 Domain of Its Adaptor Protein PDZK1.
Authors: Birrane, G. / Mulvaney, E.P. / Pal, R. / Kinsella, B.T. / Kocher, O.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Prostacyclin receptor
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Prostacyclin receptor


Theoretical massNumber of molelcules
Total (without water)24,0332
Polymers24,0332
Non-polymers00
Water2,378132
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Prostacyclin receptor


Theoretical massNumber of molelcules
Total (without water)12,0171
Polymers12,0171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Prostacyclin receptor


Theoretical massNumber of molelcules
Total (without water)12,0171
Polymers12,0171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.271, 68.477, 40.124
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Prostacyclin receptor / NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi ...NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / PDZ domain-containing protein 1 / Sodium-hydrogen exchanger regulatory factor 3 / Prostaglandin I2 receptor / PGI receptor / PGI2 receptor / Prostanoid IP receptor


Mass: 12016.534 Da / Num. of mol.: 2
Fragment: PDZ1, UNP residues 7-106, Prostacyclin receptor C-terminus, 409-415
Mutation: C10S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap70, Nherf3, Pdzk1, Prostacyclin receptor, Ptgir / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9JIL4, UniProt: P43252
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHIMERIC PDZ1-IP PROTEIN CONTAINS RESIDUES 7-106 OF PDZ1 FUSED TO THE SEVEN CARBOXY-TERMINAL AMINO ...CHIMERIC PDZ1-IP PROTEIN CONTAINS RESIDUES 7-106 OF PDZ1 FUSED TO THE SEVEN CARBOXY-TERMINAL AMINO ACIDS OF MOUSE IP (RESIDUES 409-415).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH6.5, 30% (w/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2012 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→40.1 Å / Num. all: 23390 / Num. obs: 23390 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGH

3ngh


Resolution: 1.7→40.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.118 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21914 1200 5.1 %RANDOM
Rwork0.18429 ---
all0.18611 22171 --
obs0.18611 22171 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0.1 Å2
2---0.38 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 0 132 1818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191786
X-RAY DIFFRACTIONr_bond_other_d0.0030.021233
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9892424
X-RAY DIFFRACTIONr_angle_other_deg0.89133046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.41425.51787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9811512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 87 -
Rwork0.22 1577 -
obs-23390 98.11 %

+
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://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