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- PDB-6rir: Crystal structure of phosphorylated Rab8a in complex with the Rab... -

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Basic information

Entry
Database: PDB / ID: 6rir
TitleCrystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2
Components
  • RILP-like protein 2
  • Ras-related protein Rab-8A
KeywordsSIGNALING PROTEIN / membrane trafficking / Rab GTPase / effector
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 / protein tyrosine kinase binding / axonogenesis / small monomeric GTPase / ciliary basal body / 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 / cellular response to insulin stimulus / autophagy / small GTPase binding / 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 / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
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: 1.767 Å
AuthorsWaschbusch, D. / Purlyte, E. / Alessi, D.R. / Khan, A.R.
Funding support Ireland, United Kingdom, 3items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1239 Ireland
Michael J. Fox Foundation6986 United Kingdom
Medical Research Council (United Kingdom)MC_UU_12016/2 United Kingdom
Citation
Journal: Structure / Year: 2020
Title: Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2.
Authors: Waschbusch, D. / Purlyte, E. / Pal, P. / McGrath, E. / Alessi, D.R. / Khan, A.R.
#1: Journal: Structure / Year: 2020
Title: Structural Basis for Rab8a GTPase Recruitment of RILPL2 via LRRK2-Mediated Phosphorylation of Switch 2
Authors: Waschbusch, D. / Purlyte, E. / Pal, P. / McGrath, E. / Alessi, D.R. / Khan, A.R.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Structure summary / Category: audit_author
Revision 1.2Feb 19, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
C: RILP-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0379
Polymers52,8504
Non-polymers1,1875
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-65 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.333, 71.509, 114.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABDC

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


Mass: 21129.160 Da / Num. of mol.: 2 / Mutation: Q67L
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

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Non-polymers , 4 types, 358 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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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: 51.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 8% PEG 8K 100mM Na HEPES

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.767→53.41 Å / Num. obs: 49201 / % possible obs: 99.55 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06877 / Rpim(I) all: 0.02883 / Rrim(I) all: 0.07469 / Net I/σ(I): 16.4
Reflection shellResolution: 1.767→1.83 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.9488 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 4719 / CC1/2: 0.649 / Rpim(I) all: 0.4097 / Rrim(I) all: 1.036 / % possible all: 96.33

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lhw

4lhw


Resolution: 1.767→53.41 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 21.42
RfactorNum. reflection% reflection
Rfree0.2105 4587 4.91 %
Rwork0.179 --
obs0.1805 93460 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.767→53.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 72 353 3796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073524
X-RAY DIFFRACTIONf_angle_d0.9124744
X-RAY DIFFRACTIONf_dihedral_angle_d11.1462827
X-RAY DIFFRACTIONf_chiral_restr0.056524
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.767-1.78710.33581550.30482574X-RAY DIFFRACTION87
1.7871-1.80810.32671620.29012933X-RAY DIFFRACTION100
1.8081-1.83010.24841450.26793063X-RAY DIFFRACTION100
1.8301-1.85330.28411490.26232920X-RAY DIFFRACTION100
1.8533-1.87770.24731650.25252997X-RAY DIFFRACTION100
1.8777-1.90340.29831620.25882903X-RAY DIFFRACTION100
1.9034-1.93060.30691540.25733016X-RAY DIFFRACTION100
1.9306-1.95940.27141590.23622946X-RAY DIFFRACTION100
1.9594-1.99010.2751460.23723020X-RAY DIFFRACTION100
1.9901-2.02270.24071420.21062921X-RAY DIFFRACTION100
2.0227-2.05760.27161410.20863021X-RAY DIFFRACTION100
2.0576-2.0950.24221590.20262976X-RAY DIFFRACTION100
2.095-2.13530.24431670.19062962X-RAY DIFFRACTION100
2.1353-2.17890.1991560.19022980X-RAY DIFFRACTION100
2.1789-2.22620.23051290.1872985X-RAY DIFFRACTION100
2.2262-2.2780.221480.1882996X-RAY DIFFRACTION100
2.278-2.3350.19041730.18282946X-RAY DIFFRACTION100
2.335-2.39810.21011740.17812969X-RAY DIFFRACTION100
2.3981-2.46870.20851540.17952974X-RAY DIFFRACTION100
2.4687-2.54840.28411330.19633008X-RAY DIFFRACTION100
2.5484-2.63950.20121440.18452976X-RAY DIFFRACTION100
2.6395-2.74520.20451200.17443033X-RAY DIFFRACTION100
2.7452-2.87010.1931800.17982913X-RAY DIFFRACTION100
2.8701-3.02140.21071350.17223033X-RAY DIFFRACTION100
3.0214-3.21070.22851210.16652977X-RAY DIFFRACTION100
3.2107-3.45860.19851690.1622961X-RAY DIFFRACTION100
3.4586-3.80660.19431640.15172969X-RAY DIFFRACTION100
3.8066-4.35730.17731560.14152982X-RAY DIFFRACTION100
4.3573-5.48910.16981620.14862980X-RAY DIFFRACTION100
5.4891-60.73020.19611630.18942939X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.0632 Å / Origin y: 29.7642 Å / Origin z: -6.1688 Å
111213212223313233
T0.1756 Å2-0.0026 Å20.0181 Å2-0.2322 Å2-0.0346 Å2--0.1864 Å2
L0.1937 °2-0.1648 °20.0626 °2-1.7405 °2-0.3953 °2--0.2637 °2
S0.0061 Å °-0.0132 Å °0.0188 Å °-0.0758 Å °0.0097 Å °-0.0703 Å °-0.0169 Å °0.0112 Å °-0.0084 Å °
Refinement TLS groupSelection details: all

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