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- PDB-2kwi: RalB-RLIP76 (RalBP1) complex -

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Basic information

Entry
Database: PDB / ID: 2kwi
TitleRalB-RLIP76 (RalBP1) complex
Components
  • RalA-binding protein 1
  • Ras-related protein Ral-B
KeywordsTRANSPORT PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


doxorubicin transport / regulation of exocyst localization / regulation of exocyst assembly / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / positive regulation of autophagosome assembly / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction ...doxorubicin transport / regulation of exocyst localization / regulation of exocyst assembly / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / positive regulation of autophagosome assembly / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction / ABC-type xenobiotic transporter activity / regulation of GTPase activity / positive regulation of epidermal growth factor receptor signaling pathway / small GTPase-mediated signal transduction / positive regulation of mitochondrial fission / cellular response to exogenous dsRNA / CDC42 GTPase cycle / transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / p38MAPK events / RAC1 GTPase cycle / negative regulation of protein binding / positive regulation of GTPase activity / receptor-mediated endocytosis / GTPase activator activity / cellular response to starvation / small monomeric GTPase / small GTPase binding / receptor internalization / transmembrane transport / spindle pole / chemotaxis / GDP binding / positive regulation of protein binding / positive regulation of protein phosphorylation / G protein activity / ATPase binding / midbody / Ras protein signal transduction / nuclear body / cell division / GTPase activity / apoptotic process / ubiquitin protein ligase binding / GTP binding / signal transduction / mitochondrion / extracellular exosome / 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 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Small GTPase, Ras-type ...RalA-binding protein 1 / : / RLIP76, Ral binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Ral-B / RalA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsFenwick, R.B. / Campbell, L.J. / Rajasekar, K. / Prasannan, S. / Nietlispach, D. / Camonis, J. / Owen, D. / Mott, H.R.
CitationJournal: Structure / Year: 2010
Title: The RalB-RLIP76 complex reveals a novel mode of ral-effector interaction
Authors: Fenwick, R.B. / Campbell, L.J. / Rajasekar, K. / Prasannan, S. / Nietlispach, D. / Camonis, J. / Owen, D. / Mott, H.R.
History
DepositionApr 12, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Ral-B
B: RalA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4134
Polymers26,8662
Non-polymers5472
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)51 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ras-related protein Ral-B


Mass: 20265.801 Da / Num. of mol.: 1 / Fragment: UNP residues 8-185 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALB / Production host: Escherichia coli (E. coli) / References: UniProt: P11234
#2: Protein RalA-binding protein 1 / RalBP1 / Ral-interacting protein 1 / 76 kDa Ral-interacting protein / Dinitrophenyl S-glutathione ...RalBP1 / Ral-interacting protein 1 / 76 kDa Ral-interacting protein / Dinitrophenyl S-glutathione ATPase / DNP-SG ATPase


Mass: 6600.567 Da / Num. of mol.: 1 / Fragment: UNP residues 393-446 / Mutation: C411S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALBP1, RLIP1, RLIP76 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15311
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D H(CCO)NH
1812D 1H-13C HSQC
1913D (H)CCH-TOCSY
11023D 1H-15N NOESY
11113D 1H-13C NOESY
11242D 1H-15N HSQC
11343D HNCA
11443D HNCO
11543D HN(CO)CA
11643D HN(CA)CB
11743D CBCA(CO)NH
11843D H(CCO)NH
11942D 1H-13C HSQC
12043D (H)CCH-TOCSY
12143D HBHA(CO)NH
12233D 1H-15N NOESY
12343D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate-1, 100 mM potassium chloride-2, 1 mM Magnesium chloride-3, 0.05 % sodium azide-4, 0.8 mM [U-99% 13C; U-99% 15N] RalB-5, 0.8 mM RLIP76-6, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate-7, 100 mM potassium chloride-8, 1 mM Magnesium chloride-9, 0.05 % sodium azide-10, 0.8 mM [U-99% 15N] RalB-11, 0.8 mM RLIP76-12, 90% H2O/10% D2O90% H2O/10% D2O
350 mM sodium phosphate-13, 100 mM potassium chloride-14, 1 mM Magnesium chloride-15, 0.05 % sodium azide-16, 0.8 mM [U-99% 13C; U-99% 15N] RLIP76-17, 0.8 mM RalB-18, 90% H2O/10% D2O90% H2O/10% D2O
450 mM sodium phosphate-19, 100 mM potassium chloride-20, 1 mM Magnesium chloride-21, 0.05 % sodium azide-22, 0.8 mM [U-99% 15N] RLIP76-23, 0.8 mM RalB-24, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
100 mMpotassium chloride-21
1 mMMagnesium chloride-31
0.05 %sodium azide-41
0.8 mMRalB-5[U-99% 13C; U-99% 15N]1
0.8 mMRLIP76-61
50 mMsodium phosphate-72
100 mMpotassium chloride-82
1 mMMagnesium chloride-92
0.05 %sodium azide-102
0.8 mMRalB-11[U-99% 15N]2
0.8 mMRLIP76-122
50 mMsodium phosphate-133
100 mMpotassium chloride-143
1 mMMagnesium chloride-153
0.05 %sodium azide-163
0.8 mMRLIP76-17[U-99% 13C; U-99% 15N]3
0.8 mMRalB-183
50 mMsodium phosphate-194
100 mMpotassium chloride-204
1 mMMagnesium chloride-214
0.05 %sodium azide-224
0.8 mMRLIP76-23[U-99% 15N]4
0.8 mMRalB-244
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
AzaraBoucherprocessing
AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, 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: 51

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