[English] 日本語
Yorodumi
- PDB-2ma2: Solution structure of RasGRP2 EF hands bound to calcium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ma2
TitleSolution structure of RasGRP2 EF hands bound to calcium
ComponentsRAS guanyl-releasing protein 2
KeywordsCALCIUM-BINDING PROTEIN / protein / EF hand
Function / homology
Function and homology information


diacylglycerol binding / Effects of PIP2 hydrolysis / Rap1 signalling / cellular response to calcium ion / Integrin signaling / guanyl-nucleotide exchange factor activity / positive regulation of GTPase activity / regulation of cell growth / ruffle membrane / FCERI mediated NF-kB activation ...diacylglycerol binding / Effects of PIP2 hydrolysis / Rap1 signalling / cellular response to calcium ion / Integrin signaling / guanyl-nucleotide exchange factor activity / positive regulation of GTPase activity / regulation of cell growth / ruffle membrane / FCERI mediated NF-kB activation / Ras protein signal transduction / neuron projection / lipid binding / synapse / calcium ion binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases ...RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / EF hand / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RAS guanyl-releasing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKuriyan, J. / Iwig, J. / Vercoulen, Y. / Das, R. / Barros, T. / Limnander, A. / Che, Y. / Pelton, J. / Wemmer, D. / Roose, J.
CitationJournal: Elife / Year: 2013
Title: Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1.
Authors: Iwig, J.S. / Vercoulen, Y. / Das, R. / Barros, T. / Limnander, A. / Che, Y. / Pelton, J.G. / Wemmer, D.E. / Roose, J.P. / Kuriyan, J.
History
DepositionJun 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAS guanyl-releasing protein 2


Theoretical massNumber of molelcules
Total (without water)9,2151
Polymers9,2151
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein RAS guanyl-releasing protein 2 / Calcium and DAG-regulated guanine nucleotide exchange factor I / CalDAG-GEFI / Cdc25-like protein / ...Calcium and DAG-regulated guanine nucleotide exchange factor I / CalDAG-GEFI / Cdc25-like protein / hCDC25L / F25B3.3 kinase-like protein


Mass: 9215.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASGRP2, CDC25L, MCG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LDG7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aromatic
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HNHA
1812D 1H-13C HSQC
1913D H(CCO)NH
11022D 1H-15N HSQC IPAP
11122D HN(CO)CA IPAP
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11413D 1H-15N HSQC NOE 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
1500 uM [U-99% 13C; U-99% 15N] RasGRP2, 25 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 7 % D2O, 93% H2O/7% D2O93% H2O/7% D2O
2500 uM [U-99% 13C; U-99% 15N] RasGRP2, 25 mM HEPES, 100 mM sodium chloride, 1 mM TCEP, 7 % D2O, 17 mg/mL Pf1 phage, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMRasGRP2-1[U-99% 13C; U-99% 15N]1
25 mMHEPES-21
100 mMsodium chloride-31
1 mMTCEP-41
7 %D2O-51
500 uMRasGRP2-6[U-99% 13C; U-99% 15N]2
25 mMHEPES-72
100 mMsodium chloride-82
1 mMTCEP-92
7 %D2O-102
17 mg/mLPf1 phage-112
Sample conditionsIonic strength: 0.125 / pH: 7.0 / Pressure: ambient / Temperature: 304 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
PALESZweckstetter M & Bax Adata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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