[English] 日本語
Yorodumi
- PDB-2ke5: Solution structure and dynamics of the small GTPase Ralb in its a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ke5
TitleSolution structure and dynamics of the small GTPase Ralb in its active conformation: significance for effector protein binding
ComponentsRas-related protein Ral-B
KeywordsSIGNALING PROTEIN / Ral / Cancer / Signalling / G protein / GTPase / Cell membrane / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation
Function / homology
Function and homology information


regulation of exocyst localization / regulation of exocyst assembly / positive regulation of autophagosome assembly / positive regulation of epidermal growth factor receptor signaling pathway / cellular response to exogenous dsRNA / p38MAPK events / cellular response to starvation / small monomeric GTPase / G protein activity / negative regulation of protein binding ...regulation of exocyst localization / regulation of exocyst assembly / positive regulation of autophagosome assembly / positive regulation of epidermal growth factor receptor signaling pathway / cellular response to exogenous dsRNA / p38MAPK events / cellular response to starvation / small monomeric GTPase / G protein activity / negative regulation of protein binding / positive regulation of protein serine/threonine kinase activity / receptor internalization / GDP binding / positive regulation of protein binding / midbody / ATPase binding / Ras protein signal transduction / positive regulation of protein phosphorylation / cell cycle / cell division / GTPase activity / apoptotic process / ubiquitin protein ligase binding / GTP binding / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Ral-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsFenwick, R. / Prasannan, S. / Campbell, L.J. / Nietlispach, D. / Evetts, K.A. / Camonis, J. / Mott, H.R. / Owen, D.
CitationJournal: Biochemistry / Year: 2009
Title: Solution structure and dynamics of the small GTPase RalB in its active conformation: significance for effector protein binding
Authors: Fenwick, R.B. / Prasannan, S. / Campbell, L.J. / Nietlispach, D. / Evetts, K.A. / Camonis, J. / Mott, H.R. / Owen, D.
History
DepositionJan 23, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Ras-related protein Ral-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4533
Polymers19,9061
Non-polymers5472
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Ras-related protein Ral-B


Mass: 19906.465 Da / Num. of mol.: 1 / Fragment: UNP residues 12-185 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALB / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P11234
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D HN(CO)CA
11023D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11323D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-99% 15N] RalB-1, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-2, 1 mM Magnesium chloride-3, 50 mM sodium phosphate-4, 100 mM sodium chloride-5, 0.05 % sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-99% 13C; U-99% 15N] RalB-7, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-8, 1 mM Magnesium chloride-9, 50 mM sodium phosphate-10, 100 mM sodium chloride-11, 0.05 % sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM RalB-13, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-14, 1 mM Magnesium chloride-15, 50 mM sodium phosphate-16, 100 mM sodium chloride-17, 0.05 % sodium azide-18, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRalB-1[U-99% 15N]1
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-21
1 mMMagnesium chloride-31
50 mMsodium phosphate-41
100 mMsodium chloride-51
0.05 %sodium azide-61
0.6 mMRalB-7[U-99% 13C; U-99% 15N]2
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-82
1 mMMagnesium chloride-92
50 mMsodium phosphate-102
100 mMsodium chloride-112
0.05 %sodium azide-122
0.6 mMRalB-133
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-143
1 mMMagnesium chloride-153
50 mMsodium phosphate-163
100 mMsodium chloride-173
0.05 %sodium azide-183
Sample conditionsIonic strength: 0.15 / pH: 7.6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
Azara2.7Boucherprocessing
Analysis1CCPNchemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesambiguous noe assignment
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructural calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 50 / Representative conformer: 1

+
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