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- PDB-6stf: Human Rab8a phosphorylated at Ser111 in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 6stf
TitleHuman Rab8a phosphorylated at Ser111 in complex with GDP
ComponentsRas-related protein Rab-8A
KeywordsSIGNALING PROTEIN / Parkinson Disease / Phosphorylation / Small G-Protein / SF3 Motif
Function / homology
Function and homology information


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 / protein localization to cilium / myosin V binding / RAB geranylgeranylation / vesicle docking involved in exocytosis ...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 / protein localization to cilium / myosin V binding / RAB geranylgeranylation / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / non-motile cilium / regulation of exocytosis / endocytic recycling / TBC/RABGAPs / ciliary membrane / Golgi organization / ciliary base / cilium assembly / protein secretion / phagocytic vesicle / trans-Golgi network membrane / Anchoring of the basal body to the plasma membrane / small monomeric GTPase / protein tyrosine kinase binding / axonogenesis / centriole / regulation of autophagy / ciliary basal body / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cilium / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / small GTPase binding / GDP binding / recycling endosome membrane / cellular response to insulin stimulus / autophagy / phagocytic vesicle membrane / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / dendritic spine / postsynaptic density / endosome / GTPase activity / centrosome / Golgi membrane / glutamatergic synapse / intracellular membrane-bounded organelle / neuronal cell body / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVieweg, S. / Mulholland, K. / Braeuning, B. / Kachariya, N. / Lai, Y. / Toth, R. / Sattler, M. / Groll, M. / Itzen, A. / Muqit, M.M.K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Biochem.J. / Year: 2020
Title: PINK1-dependent phosphorylation of Serine111 within the SF3 motif of Rab GTPases impairs effector interactions and LRRK2-mediated phosphorylation at Threonine72.
Authors: Vieweg, S. / Mulholland, K. / Brauning, B. / Kachariya, N. / Lai, Y.C. / Toth, R. / Singh, P.K. / Volpi, I. / Sattler, M. / Groll, M. / Itzen, A. / Muqit, M.M.K.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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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
C: Ras-related protein Rab-8A
D: Ras-related protein Rab-8A
E: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,96615
Polymers103,6285
Non-polymers2,33810
Water81145
1
A: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1933
Polymers20,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1933
Polymers20,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1933
Polymers20,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1933
Polymers20,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1933
Polymers20,7261
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.550, 75.180, 107.700
Angle α, β, γ (deg.)90.000, 100.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20725.699 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P61006
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35267 / % possible obs: 97.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4015 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LHV
Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.911 / SU B: 23.313 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1763 5 %RANDOM
Rwork0.2328 ---
obs0.2343 33488 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.09 Å2 / Biso mean: 48.379 Å2 / Biso min: 25.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å21.04 Å2
2--0.01 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6685 0 145 45 6875
Biso mean--36.68 39.45 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136930
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176560
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.6739315
X-RAY DIFFRACTIONr_angle_other_deg1.051.60415172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78422.326374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.383151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2461548
X-RAY DIFFRACTIONr_chiral_restr0.0340.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021518
X-RAY DIFFRACTIONr_rigid_bond_restr0.187313489
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 126 -
Rwork0.375 2396 -
all-2522 -
obs--97.19 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.08380.22820.0020.67150.08580.5085-0.008-0.01450.0167-0.0202-0.02770.03810.00620.03320.03570.00810.0044-0.03210.2077-0.00590.1396-16.983289.62327.1574
20.73860.23280.00260.3701-0.11120.7348-0.0046-0.0209-0.1082-0.0154-0.0125-0.05520.04610.01570.01710.0325-0.0124-0.05310.1918-0.02120.1352-17.904637.772837.7266
30.28350.3764-0.30530.7109-0.13010.6923-0.01620.0263-0.01170.00020.0566-0.07070.0409-0.0239-0.04030.02460.0092-0.05550.2322-0.01680.13468.013252.099612.7399
41.3376-0.1795-0.21080.4165-0.27310.3336-0.1031-0.18030.03620.00530.05730.01030.01410.08340.04590.02920.0239-0.0450.2430.00070.123112.087267.017541.8448
50.50550.17570.57351.2259-0.16890.7707-0.0153-0.04740.0110.04660.03070.0289-0.0297-0.0762-0.01540.01470.0306-0.03150.2134-0.00410.1212-23.427668.940628.1773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 902
2X-RAY DIFFRACTION2B5 - 902
3X-RAY DIFFRACTION3C6 - 902
4X-RAY DIFFRACTION4D7 - 902
5X-RAY DIFFRACTION5E6 - 902

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