[English] 日本語
Yorodumi
- PDB-1gq5: Structural Determinants of the NHERF Interaction with beta2-AR an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gq5
TitleStructural Determinants of the NHERF Interaction with beta2-AR and PDGFR
ComponentsEZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50
KeywordsSIGNALING PROTEIN / PDZ / BETA2-ADRENERGIC RECEPTOR / PDGFR / NHERF / COMPLEX
Function / homology
Function and homology information


platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / dopamine receptor binding / smooth muscle cell chemotaxis / import across plasma membrane / channel activator activity ...platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / dopamine receptor binding / smooth muscle cell chemotaxis / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / metanephric glomerular capillary formation / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / cell migration involved in vasculogenesis / negative regulation of sodium ion transport / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / aorta morphogenesis / bile acid secretion / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / maintenance of epithelial cell apical/basal polarity / intracellular phosphate ion homeostasis / cilium organization / retina vasculature development in camera-type eye / plasma membrane organization / stereocilium tip / vascular endothelial growth factor binding / cardiac myofibril assembly / gland morphogenesis / myosin II binding / phosphatidylinositol metabolic process / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / establishment of Golgi localization / positive regulation of chemotaxis / fibroblast migration / Signaling by PDGF / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / platelet-derived growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / chloride channel regulator activity / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / beta-2 adrenergic receptor binding / microvillus membrane / positive regulation of DNA biosynthetic process / regulation of cell size / renal absorption / positive regulation of smooth muscle cell migration / positive regulation of calcium ion import / platelet-derived growth factor receptor-beta signaling pathway / microvillus / positive regulation of phosphoprotein phosphatase activity / transport across blood-brain barrier / platelet-derived growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endomembrane system / phosphatase binding / positive regulation of phospholipase C activity / positive regulation of calcium-mediated signaling / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / cell chemotaxis / Downstream signal transduction / lysosomal lumen / positive regulation of mitotic nuclear division / filopodium / PDZ domain binding / cell periphery / protein localization to plasma membrane / regulation of actin cytoskeleton organization / morphogenesis of an epithelium / brush border membrane / sensory perception of sound / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / receptor protein-tyrosine kinase / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of reactive oxygen species metabolic process
Similarity search - Function
Platelet-derived growth factor receptor beta / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / PDZ domain / Pdz3 Domain / Immunoglobulin / Immunoglobulin domain ...Platelet-derived growth factor receptor beta / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / PDZ domain / Pdz3 Domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / PDZ domain / Immunoglobulin subtype 2 / PDZ domain profile. / Immunoglobulin C-2 Type / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Platelet-derived growth factor receptor beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarthikeyan, S. / Leung, T. / Ladias, J.A.A.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structural Determinants of the Na+/H+ Exchanger Regulatory Factor Interaction with the Beta 2 Adrenergic and Platelet-Derived Growth Factor Receptors
Authors: Karthikeyan, S. / Leung, T. / Ladias, J.A.A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Structural Basis of the Na+/H+ Exchanger Regulatory Factor Pdz1 Interaction with the Carboxyl-Terminal Region of the Cystic Fibrosis Transmembrabe Conductance Regulator
Authors: Karthikeyan, S. / Leung, T. / Ladias, J.A.A.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of the Pdz1 Domain of Human Na+/ H+ Exchanger Regulatory Factor Provides Insights Into the Mechanism of Carboxyl-Terminal Leucine Recognition by Class I Pdz Domains
Authors: Karthikeyan, S. / Leung, T. / Birrane, G. / Webster, G. / Ladias, J.A.A.
History
DepositionNov 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0193
Polymers9,9481
Non-polymers712
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.073, 50.073, 66.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein EZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50 / NA+/H+ EXCHANGER REGULATORY FACTOR


Mass: 9948.382 Da / Num. of mol.: 1 / Fragment: PDZ1 DOMAIN, RESIDUES 11-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14745, UniProt: P09619
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 9-10 ARE CLONING ARTIFACTS. THE AMINO ACID RESIDUES 95-99 OF PDZ1 CORRESPOND TO THE ...RESIDUES 9-10 ARE CLONING ARTIFACTS. THE AMINO ACID RESIDUES 95-99 OF PDZ1 CORRESPOND TO THE CARBOXYL-TERMINAL REGION 1102-1106 OF PDGFR AND SERVE AS A LIGAND FOR A NEIGHBOURING PDZ1 MOLECULE IN THE CRYSTAL.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.6 / Details: SODIUM ACETATE, SODIUM CHLORIDE, pH 4.60

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 3, 2001 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→26.4 Å / Num. obs: 4966 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 85.6

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I92

1i92


Resolution: 2.2→26.4 Å / SU B: 8.267 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.234
RfactorNum. reflection% reflectionSelection details
Rfree0.263 268 5.4 %RANDOM
Rwork0.222 ---
obs0.225 4690 99.9 %-
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.68 Å20 Å2
2--1.37 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 2 55 739

+
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