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- PDB-7lwb: Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) ... -

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Basic information

Entry
Database: PDB / ID: 7lwb
TitleCrystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2
Components
  • RILP-like protein 2
  • Ras-related protein Rab-8A
KeywordsSIGNALING PROTEIN / membrane trafficking / Rab8a / effector / Rab-interacting lysosomal protein-like 2 / macromolecular complex / LRRK2 kinase / switch 2 / phosphorylation ciliogenesis
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 / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / epithelial cell morphogenesis / RAB geranylgeranylation / myosin V binding ...protein transport from ciliary membrane to plasma membrane / neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / epithelial cell morphogenesis / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / non-motile cilium / dynein light intermediate chain binding / endocytic recycling / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / protein secretion / cilium assembly / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / centriole / axonogenesis / small monomeric GTPase / ciliary basal body / trans-Golgi network membrane / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to 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 / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rab interacting lysosomal protein, dimerization domain / Rab interacting lysosomal protein / RH1 domain / RH2 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 ...Rab interacting lysosomal protein, dimerization domain / Rab interacting lysosomal protein / RH1 domain / RH2 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: 1.9 Å
AuthorsWaschbusch, D. / Khan, A.R.
CitationJournal: Biophys.J. / Year: 2021
Title: Dual arginine recognition of LRRK2 phosphorylated Rab GTPases.
Authors: Waschbusch, D. / Purlyte, E. / Khan, A.R.
History
DepositionFeb 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: 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
D: RILP-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8264
Polymers27,2782
Non-polymers5472
Water1,24369
1
A: Ras-related protein Rab-8A
D: RILP-like protein 2
hetero molecules

A: Ras-related protein Rab-8A
D: RILP-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6518
Polymers54,5564
Non-polymers1,0954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7270 Å2
ΔGint-72 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.773, 68.430, 128.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 21129.160 Da / Num. of mol.: 1 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Details: T72 is phosphorylated (TPO) / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli (E. coli) / References: UniProt: P61006
#2: Protein RILP-like protein 2 / Rab-interacting lysosomal protein-like 2 / p40phox-binding protein


Mass: 6149.065 Da / Num. of mol.: 1 / Fragment: RH2 domain
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 / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7.5 / Details: 150mM DL-Malic acid, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→46.26 Å / Num. obs: 21414 / % possible obs: 96.02 % / Redundancy: 8.6 % / Biso Wilson estimate: 43.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05713 / Rpim(I) all: 0.02056 / Net I/σ(I): 16.79
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 7.9 % / Rmerge(I) obs: 4.301 / Mean I/σ(I) obs: 0.35 / Num. unique obs: 1964 / CC1/2: 0.54 / Rpim(I) all: 1.62 / Rrim(I) all: 4.61 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rir

6rir


Resolution: 1.9→46.26 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 39.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1044 4.92 %
Rwork0.2187 38198 -
obs0.2209 21268 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.9 Å2 / Biso mean: 58.0008 Å2 / Biso min: 37.04 Å2
Refinement stepCycle: final / Resolution: 1.9→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 33 69 1883
Biso mean--48.17 53.94 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141862
X-RAY DIFFRACTIONf_angle_d1.3292510
X-RAY DIFFRACTIONf_dihedral_angle_d23.379262
X-RAY DIFFRACTIONf_chiral_restr0.076278
X-RAY DIFFRACTIONf_plane_restr0.007314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.56551450.55082381252684
1.95-20.54931730.476728212994100
2-2.060.48431570.406428222979100
2.06-2.130.46231580.3672840299899
2.13-2.20.3621620.324828473009100
2.2-2.290.3639910.31621898198967
2.29-2.390.27561210.255228672988100
2.39-2.520.31211220.25082839296199
2.52-2.680.31691500.246228613011100
2.68-2.880.32831600.251928342994100
2.88-3.170.34041220.238828692991100
3.17-3.630.24031490.21812821297099
3.67-4.580.21761330.16782641277499
4.58-46.260.17151320.157528572989100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.95250.93080.01974.12281.39363.2617-0.0896-0.1471-0.01560.4431-0.10660.38280.233-0.22170.17350.378-0.03890.03730.3891-0.03660.3471-13.3513-17.1088-13.1147
23.1286-0.9365-0.32662.83460.04092.77050.0379-0.0094-0.0245-0.4043-0.05630.3905-0.12880.04290.02370.3474-0.00770.01280.4714-0.0180.3261-1.8228-17.2599-31.3278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 0:179)A0 - 179
2X-RAY DIFFRACTION2(chain D and resseq 126:161)D126 - 161

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