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- PDB-2mbg: Rlip76 (gap-gbd) -

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Basic information

Entry
Database: PDB / ID: 2mbg
TitleRlip76 (gap-gbd)
ComponentsRalA-binding protein 1
KeywordsPROTEIN BINDING / RhoGAP / RalBP1
Function / homology
Function and homology information


doxorubicin transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction / positive regulation of mitochondrial fission / small GTPase-mediated signal transduction ...doxorubicin transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction / positive regulation of mitochondrial fission / small GTPase-mediated signal transduction / regulation of GTPase activity / xenobiotic transmembrane transporter activity / CDC42 GTPase cycle / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / RAC1 GTPase cycle / GTPase activator activity / transmembrane transport / small GTPase binding / positive regulation of GTPase activity / spindle pole / endocytosis / chemotaxis / nuclear body / positive regulation of protein phosphorylation / mitochondrion / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
RalA-binding protein 1 / : / RLIP76, Ral binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases ...RalA-binding protein 1 / : / RLIP76, Ral binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RalA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsRajasekar, K.V. / Campbell, L.J. / Nietlispach, D. / Owen, D. / Mott, H.R.
CitationJournal: Structure / Year: 2013
Title: The Structure of the RLIP76 RhoGAP-Ral Binding Domain Dyad: Fixed Position of the Domains Leads to Dual Engagement of Small G Proteins at the Membrane.
Authors: Rajasekar, K.V. / Campbell, L.J. / Nietlispach, D. / Owen, D. / Mott, H.R.
History
DepositionJul 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RalA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)31,0151
Polymers31,0151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein RalA-binding protein 1 / RalBP1 / 76 kDa Ral-interacting protein / Dinitrophenyl S-glutathione ATPase / DNP-SG ATPase / Ral- ...RalBP1 / 76 kDa Ral-interacting protein / Dinitrophenyl S-glutathione ATPase / DNP-SG ATPase / Ral-interacting protein 1


Mass: 31015.139 Da / Num. of mol.: 1 / Fragment: UNP residues 184-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALBP1, RLIP1, RLIP76 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15311

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N-TROSY
1243D HNCA
1343D HN(CO)CA
1443D HN(CA)CB
1543D HN(COCA)CB
1643D HNCO
1723D 1H-15N NOESY
1833D HBHA(CBCACO)NH
1933D (H)CCH-TOCSY
11033D (H)CCH-TOCSY
11133D 1H-13C NOESY
11232D 1H-13C HSQC
11333D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM RLIP76-GAP-GBD, 20 mM TRIS, 100 mM sodium chloride, 0.05 % sodium azide, 5 mM DTT, 90 % H20, 10 % D20, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-100% 15N] RLIP76-GAP-GBD, 20 mM TRIS, 100 mM sodium chloride, 0.05 % sodium azide, 5 mM DTT, 90 % H20, 10 % D20, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM [U-100% 13C; U-100% 15N] RLIP76-GAP-GBD, 20 mM TRIS, 100 mM sodium chloride, 0.05 % sodium azide, 5 mM DTT, 90 % H20, 10 % D20, 90% H2O/10% D2O90% H2O/10% D2O
40.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] RLIP76-GAP-GBD, 20 mM TRIS, 100 mM sodium chloride, 0.05 % sodium azide, 5 mM DTT, 90 % H20, 10 % D20, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRLIP76-GAP-GBD-11
20 mMTRIS-21
100 mMsodium chloride-31
0.05 %sodium azide-41
5 mMDTT-51
90 %H20-61
10 %D20-71
0.7 mMRLIP76-GAP-GBD-8[U-100% 15N]2
20 mMTRIS-92
100 mMsodium chloride-102
0.05 %sodium azide-112
5 mMDTT-122
90 %H20-132
10 %D20-142
0.6 mMRLIP76-GAP-GBD-15[U-100% 13C; U-100% 15N]3
20 mMTRIS-163
100 mMsodium chloride-173
0.05 %sodium azide-183
5 mMDTT-193
90 %H20-203
10 %D20-213
0.4 mMRLIP76-GAP-GBD-22[U-100% 13C; U-100% 15N; U-80% 2H]4
20 mMTRIS-234
100 mMsodium chloride-244
0.05 %sodium azide-254
5 mMDTT-264
90 %H20-274
10 %D20-284
Sample conditionspH: 7.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
AzaraBoucherprocessing
CCPN-Analysis(CCPN)- Vranken et al.chemical shift assignment
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ARIA based water refinement
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: 35

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