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- PDB-6whe: Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state -

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Basic information

Entry
Database: PDB / ID: 6whe
TitleStructure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state
ComponentsRas-related protein Rab-8A
KeywordsSIGNALING PROTEIN / HYDROLASE / Rab GTPase / membrane trafficking / Leucine-rich repeat kinase 2 (LRRK2) / switch 2 phosphorylation / effector recruitment / Golgi membranes / ciliogenesis / Parkinson's disease / Rab-interacting lysosomal protein-like 2 (RILPL2)
Function / homology
Function and homology information


neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / endocytic recycling / vesicle docking involved in exocytosis / non-motile cilium / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / axoneme / phagocytic vesicle / axonogenesis / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / trans-Golgi network membrane / small monomeric GTPase / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / centriole / regulation of long-term neuronal synaptic plasticity / autophagy / phagocytic vesicle membrane / small GTPase binding / recycling endosome membrane / centriolar satellite / cellular response to insulin stimulus / synaptic vesicle / GDP binding / Regulation of PLK1 Activity at G2/M Transition / actin cytoskeleton / G protein activity / midbody / lysosome / endosome membrane / endosome / cilium / ciliary basal body / Golgi membrane / neuronal cell body / GTPase activity / centrosome / dendrite / GTP binding / nucleolus / glutamatergic synapse / Golgi apparatus / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
: / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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
DepositionApr 8, 2020Deposition 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-8A
B: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3417
Polymers42,1542
Non-polymers1,1875
Water5,693316
1
A: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6253
Polymers21,0771
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7174
Polymers21,0771
Non-polymers6403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.092, 118.377, 39.603
Angle α, β, γ (deg.)90.000, 101.960, 90.000
Int Tables number4
Space group name H-MP1211

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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, small monomeric GTPase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 316 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 20% PEG3350, 0.1M Hepes pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979279 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979279 Å / Relative weight: 1
ReflectionResolution: 1.72→29.29 Å / Num. obs: 144140 / % possible obs: 96 % / Redundancy: 4.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.072 / Rrim(I) all: 0.154 / Net I/σ(I): 6.9
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.441 / Num. unique obs: 1551 / CC1/2: 0.806 / Rpim(I) all: 0.25 / Rrim(I) all: 0.51 / % possible all: 85.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lhw

4lhw


Resolution: 1.73→29.29 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 23.77
RfactorNum. reflection% reflection
Rfree0.2304 1632 4.99 %
Rwork0.1866 --
obs0.1888 32684 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.05 Å2 / Biso mean: 19.8405 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.73→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 72 316 3198
Biso mean--14.64 29.12 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062939
X-RAY DIFFRACTIONf_angle_d0.8593959
X-RAY DIFFRACTIONf_dihedral_angle_d25.581114
X-RAY DIFFRACTIONf_chiral_restr0.056436
X-RAY DIFFRACTIONf_plane_restr0.004489
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.73-1.750.28961030.2378218281
1.75-1.780.26471490.2147278598
1.78-1.810.27691370.2114276298
1.81-1.840.25151780.2028267098
1.84-1.870.22571290.2109270397
1.87-1.910.31161560.2192279898
1.91-1.950.2631460.2113263497
1.95-1.990.23421560.1954277497
1.99-2.040.24761260.1864266297
2.04-2.090.20751450.192268095
2.09-2.140.2371320.1935265896
2.14-2.210.23841480.1944267796
2.21-2.280.26291330.2156270796
2.28-2.360.25441160.202264594
2.36-2.450.23861410.192256793
2.45-2.560.22061350.1949263094
2.56-2.70.27691290.1904256893
2.7-2.870.28541270.19258492
2.87-3.090.21921240.1853253490
3.09-3.40.17981200.1687247989
3.4-3.890.2161580.1649252091
3.89-4.90.18631270.1476245788
Refinement TLS params.Method: refined / Origin x: -12.2038 Å / Origin y: -30.4102 Å / Origin z: 1.4229 Å
111213212223313233
T0.0765 Å2-0.0095 Å2-0.0133 Å2-0.1062 Å2-0.0032 Å2--0.0998 Å2
L0.1683 °20.0292 °2-0.1317 °2-0.6047 °2-0.2037 °2--0.6621 °2
S-0.0001 Å °-0.0049 Å °0.0094 Å °0.0286 Å °0.0075 Å °-0.0034 Å °0.0297 Å °-0.0265 Å °-0.0028 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 175
2X-RAY DIFFRACTION1allX900 - 901
3X-RAY DIFFRACTION1allB4 - 178
4X-RAY DIFFRACTION1allC900 - 901
5X-RAY DIFFRACTION1allG401
6X-RAY DIFFRACTION1allS1 - 319

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