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- PDB-6zqt: Crystal structure of the RLIP76 Ral binding domain mutant (E427H/... -

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Basic information

Entry
Database: PDB / ID: 6zqt
TitleCrystal structure of the RLIP76 Ral binding domain mutant (E427H/Q433L/K440R) in complex with RalB-GMPPNP
Components
  • RalA-binding protein 1
  • Ras-related protein Ral-B
KeywordsPROTEIN BINDING / RalB / RLIP76 / Ral binding domain / coiled-coil / small GTPase / G protein
Function / homology
Function and homology information


regulation of exocyst localization / doxorubicin transport / 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 / regulation of Cdc42 protein signal transduction / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity ...regulation of exocyst localization / doxorubicin transport / 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 / regulation of Cdc42 protein signal transduction / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / regulation of small GTPase mediated signal transduction / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / small GTPase-mediated signal transduction / cellular response to exogenous dsRNA / regulation of GTPase activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / CDC42 GTPase cycle / ATPase-coupled transmembrane transporter activity / p38MAPK events / RAC1 GTPase cycle / cellular response to starvation / GTPase activator activity / small monomeric GTPase / G protein activity / negative regulation of protein binding / positive regulation of protein serine/threonine kinase activity / transmembrane transport / receptor internalization / small GTPase binding / positive regulation of GTPase activity / spindle pole / endocytosis / GDP binding / chemotaxis / positive regulation of protein binding / midbody / ATPase binding / Ras protein signal transduction / nuclear body / cell cycle / positive regulation of protein phosphorylation / 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 / 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. ...RalA-binding protein 1 / : / RLIP76, Ral binding domain / 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 / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Ral-B / RalA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsHurd, C. / Brear, P. / Revell, J. / Ross, S. / Mott, H. / Owen, D.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPases.
Authors: Hurd, C.A. / Brear, P. / Revell, J. / Ross, S. / Mott, H.R. / Owen, D.
History
DepositionJul 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,9629
Polymers55,7774
Non-polymers1,1855
Water6,503361
1
A: Ras-related protein Ral-B
C: RalA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5275
Polymers27,8892
Non-polymers6393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Ral-B
D: RalA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4354
Polymers27,8892
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.450, 77.430, 66.400
Angle α, β, γ (deg.)90.000, 90.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Ral-B


Mass: 20998.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P11234
#2: 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: 6889.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALBP1, RLIP1, RLIP76 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q15311

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Non-polymers , 4 types, 366 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine 9.0 pH, 30% w/v PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→50.404 Å / Num. obs: 75045 / % possible obs: 99.7 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.022 / Rrim(I) all: 0.065 / Net I/σ(I): 18.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.51-1.554.51.0562466254760.6240.5521.1951.298.7
6.75-50.48.20.05571598710.9930.020.05968.299.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KWI

2kwi


Resolution: 1.51→50.404 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 3763 5.02 %
Rwork0.1885 71247 -
obs0.1901 75010 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.78 Å2 / Biso mean: 34.4674 Å2 / Biso min: 17.13 Å2
Refinement stepCycle: final / Resolution: 1.51→50.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 72 362 4100
Biso mean--25.35 40.35 -
Num. residues----452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.51-1.52910.40261110.3617261398
1.5291-1.54930.36721260.329262599
1.5493-1.57050.34161410.3099261099
1.5705-1.59290.31241460.3091260999
1.5929-1.61670.29481520.2906259499
1.6167-1.6420.30541670.26682610100
1.642-1.66890.29371540.252260599
1.6689-1.69770.28231570.2431262699
1.6977-1.72850.24171340.23242594100
1.7285-1.76180.22661420.22252656100
1.7618-1.79770.26181230.21472608100
1.7977-1.83680.27331280.20692649100
1.8368-1.87960.21811240.20392665100
1.8796-1.92660.21411190.19662648100
1.9266-1.97870.23151480.19162654100
1.9787-2.03690.24431230.19632657100
2.0369-2.10260.2111850.18892571100
2.1026-2.17780.24321260.19332666100
2.1778-2.2650.22931370.18832654100
2.265-2.36810.22391350.19072670100
2.3681-2.49290.24031360.19742648100
2.4929-2.64910.24821640.1932626100
2.6491-2.85360.23391620.19872606100
2.8536-3.14070.1948980.1882729100
3.1407-3.59510.19381370.1722663100
3.5951-4.5290.19031320.1472690100
4.529-50.4040.19611560.17552701100

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