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- PDB-6sq2: Structure of a phosphomimetic switch 2 variant of Rab8a in comple... -

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Basic information

Entry
Database: PDB / ID: 6sq2
TitleStructure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2
Components
  • RILP-like protein 2
  • Ras-related protein Rab-8A
KeywordsSIGNALING PROTEIN / Rab8a GTPases / effector / RILP-like protein 2 / signaling complex / LRRK2 protein kinase / ciliogenesis / Parkinson's disease
Function / homology
Function and homology information


protein transport from ciliary membrane to plasma membrane / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / epithelial cell morphogenesis / myosin V binding / RAB geranylgeranylation ...protein transport from ciliary membrane to plasma membrane / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / epithelial cell morphogenesis / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / dynein light intermediate chain binding / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / protein secretion / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / protein tyrosine kinase binding / ciliary basal body / small monomeric GTPase / trans-Golgi network membrane / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / autophagy / small GTPase binding / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / dendritic spine / postsynaptic density / protein dimerization activity / endosome membrane / endosome / Golgi membrane / GTPase activity / neuronal cell body / centrosome / glutamatergic synapse / GTP binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rab interacting lysosomal protein, dimerization domain / Rab interacting lysosomal protein / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. ...Rab interacting lysosomal protein, dimerization domain / Rab interacting lysosomal protein / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 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
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-8A / RILP-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 Å
AuthorsKhan, A.R. / Waschbusch, D.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1239 Ireland
CitationJournal: To Be Published
Title: Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2
Authors: Khan, A.R. / Waschbusch, D.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 Rab-8A
B: Ras-related protein Rab-8A
D: RILP-like protein 2
E: RILP-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8418
Polymers52,7464
Non-polymers1,0954
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-60 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.698, 71.733, 116.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rab-8A / Oncogene c-mel


Mass: 21077.191 Da / Num. of mol.: 2 / Mutation: Q67L, T72E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli (E. coli) / References: UniProt: P61006
#2: Protein/peptide RILP-like protein 2 / Rab-interacting lysosomal protein-like 2 / p40phox-binding protein


Mass: 5296.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RILPL2, RLP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969X0
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM HEPES 10% PEG 4,000 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.68→61.07 Å / Num. obs: 56711 / % possible obs: 97.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 17.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.025 / Rrim(I) all: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2 % / Rmerge(I) obs: 0.402 / Num. unique obs: 2041 / CC1/2: 0.616 / Rpim(I) all: 0.323 / Rrim(I) all: 0.52 / % possible all: 69.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lhw

4lhw


Resolution: 1.684→61.067 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.2023 5300 5.09 %
Rwork0.1815 --
obs0.1825 56711 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.12 Å2 / Biso mean: 24.9565 Å2 / Biso min: 8.5 Å2
Refinement stepCycle: final / Resolution: 1.684→61.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 66 513 3944
Biso mean--14.15 36.21 -
Num. residues----412
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.684-1.70260.4077800.3579159445
1.7026-1.72270.38251210.344254472
1.7227-1.74370.31811470.3051276378
1.7437-1.76570.28851920.2504302688
1.7657-1.7890.22771740.2136343997
1.789-1.81350.21422010.1903349399
1.8135-1.83940.20382020.1833497100
1.8394-1.86690.20671990.1914347899
1.8669-1.8960.23681980.2321336296
1.896-1.92710.35451570.2964297485
1.9271-1.96040.2871570.2347329492
1.9604-1.9960.22081670.18093538100
1.996-2.03440.21421980.1816344299
2.0344-2.07590.22271490.2157316688
2.0759-2.12110.25791870.1917335497
2.1211-2.17040.23781990.183549100
2.1704-2.22470.22861730.17633504100
2.2247-2.28480.21371590.2062314389
2.2848-2.35210.18262170.1683478100
2.3521-2.4280.1631870.16363536100
2.428-2.51480.21521980.1746343599
2.5148-2.61550.20581850.1823518100
2.6155-2.73450.21571650.1862344197
2.7345-2.87870.21021670.18023527100
2.8787-3.0590.1791710.167350399
3.059-3.29520.15541810.1683347899
3.2952-3.62680.17912140.1638340897
3.6268-4.15150.14721920.1491335896
4.1515-5.230.1531980.1436346799
5.23-61.0670.25181650.1817350699
Refinement TLS params.Method: refined / Origin x: -9.1724 Å / Origin y: -65.9984 Å / Origin z: 6.0629 Å
111213212223313233
T0.0933 Å2-0.0022 Å2-0.0084 Å2-0.1247 Å2-0.0177 Å2--0.0871 Å2
L0.1175 °20.012 °2-0.0243 °2-1.4283 °2-0.3497 °2--0.0961 °2
S-0.0149 Å °0.0131 Å °0.0116 Å °0.0093 Å °0.0288 Å °-0.038 Å °0.0055 Å °-0.0016 Å °-0.0031 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 177
2X-RAY DIFFRACTION1allX900 - 901
3X-RAY DIFFRACTION1allB4 - 176
4X-RAY DIFFRACTION1allY900 - 901
5X-RAY DIFFRACTION1allD129 - 159
6X-RAY DIFFRACTION1allE129 - 160
7X-RAY DIFFRACTION1allS1 - 540

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