[English] 日本語
Yorodumi
- PDB-2os6: Solution structure of LARG PDZ domain in complex with C-terminal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2os6
TitleSolution structure of LARG PDZ domain in complex with C-terminal octa-peptide of Plexin B1
Components
  • C-terminal peptide of Plexin-B1
  • Rho guanine nucleotide exchange factor 12
KeywordsCELL ADHESION / nerve system development / cytoskeleton rearrangement
Function / homology
Function and homology information


Rho-activating G protein-coupled receptor signaling pathway / semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / negative regulation of cell adhesion / semaphorin receptor activity / GTPase activating protein binding / RHOD GTPase cycle / inhibitory synapse assembly / Sema4D induced cell migration and growth-cone collapse ...Rho-activating G protein-coupled receptor signaling pathway / semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / negative regulation of cell adhesion / semaphorin receptor activity / GTPase activating protein binding / RHOD GTPase cycle / inhibitory synapse assembly / Sema4D induced cell migration and growth-cone collapse / positive regulation of axonogenesis / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / RHOB GTPase cycle / NRAGE signals death through JNK / positive regulation of Rho protein signal transduction / RHOC GTPase cycle / regulation of cytoskeleton organization / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / RHOA GTPase cycle / Rho protein signal transduction / synapse assembly / positive regulation of GTPase activity / GTPase activator activity / neuron projection morphogenesis / regulation of cell migration / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / transmembrane signaling receptor activity / cell migration / G alpha (12/13) signalling events / regulation of cell shape / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / G protein-coupled receptor signaling pathway / glutamatergic synapse / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ARHGEF12, PH domain / LARG, RGS domain / Plexin-B, PSI domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Plexin A/B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain ...ARHGEF12, PH domain / LARG, RGS domain / Plexin-B, PSI domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Plexin A/B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / ARHGEF1-like, PH domain / PH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Plexin family / Plexin repeat / Plexin repeat / RGS, subdomain 2 / Sema domain / semaphorin domain / Sema domain / RGS domain superfamily / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / PDZ domain / Pdz3 Domain / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Immunoglobulin E-set / Roll / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Plexin-B1 / Rho guanine nucleotide exchange factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsLiu, J. / Huang, H. / Yang, Y.
CitationJournal: To be Published
Title: Solution structure of the LARG PDZ domain in complex with C-terminal peptide of Plexin B1
Authors: Liu, J. / Huang, H. / Yang, Y.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 12
B: C-terminal peptide of Plexin-B1


Theoretical massNumber of molelcules
Total (without water)10,2882
Polymers10,2882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Rho guanine nucleotide exchange factor 12 / LARG protein / Leukemia-associated RhoGEF


Mass: 9369.684 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b (+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NZN5
#2: Protein/peptide C-terminal peptide of Plexin-B1 / Semaphorin receptor SEP


Mass: 918.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: O43157

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1322D, 13C, 15N-filtered, 13C-edited NOESY
142DQF-COSY
1522D TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 90% H2O, 10% D2O50mM phosphate buffer, 90% H2O, 10% D2O
20.8mM 15N, 13C-labeled LARG PDZ domain, 5mM EDTA, 1mM DTT, 7.6mM synthetic peptide, 50mM phosphate buffer, 99.9% D2O50mM phosphate buffer, 99.9% D2O
Sample conditionsIonic strength: 50 mM phosphate buffer, 50mM NaCl / pH: 6 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNSCns 1.1Brunger A. T. etallstructure solution
NMRPipeNmrpipe 2.2F.Delaglioprocessing
Sparky 3Sparky 3T.D.Goddard and D.G.Knellerdata analysis
Molmol 2k.2Molmol 2k.2Koradiprocessing
Csi 1.0Csi 1.0David S. Wishartrefinement
RefinementMethod: Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The complex structure is solved using a total of 1306 experimental restraints that include 1155 intramolecular NOEs, 90 dihedral angle restraints and 61 intermolecular NOEs derived from NMR spectroscopy
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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