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- PDB-6stg: Human Rab8a phosphorylated at Ser111 in complex with GPPNP -

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Basic information

Entry
Database: PDB / ID: 6stg
TitleHuman Rab8a phosphorylated at Ser111 in complex with GPPNP
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 / regulation of protein transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / 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 / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / protein localization to cilium / endocytic recycling / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / exocytosis / cilium assembly / phagocytic vesicle / centriole / axonogenesis / Anchoring of the basal body to the plasma membrane / protein tyrosine kinase binding / trans-Golgi network membrane / small monomeric GTPase / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / small GTPase binding / autophagy / centriolar satellite / cellular response to insulin stimulus / phagocytic vesicle membrane / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / GDP binding / actin cytoskeleton / midbody / endosome membrane / lysosome / endosome / regulation of autophagy / ciliary basal body / cilium / Golgi membrane / neuronal cell body / GTPase activity / dendrite / centrosome / 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 ...: / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Revision 1.2Jan 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)42,6677
Polymers41,4512
Non-polymers1,2155
Water1629
1
A: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2723
Polymers20,7261
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)21,3944
Polymers20,7261
Non-polymers6693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.920, 93.720, 56.120
Angle α, β, γ (deg.)90.000, 102.970, 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: 20725.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61006
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 30% PEG300

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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: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 11734 / % possible obs: 95.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2 / Num. unique obs: 1222

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LHW

4lhw


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.896 / SU B: 37.08 / SU ML: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 586 5 %RANDOM
Rwork0.2426 ---
obs0.2454 11143 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.83 Å2 / Biso mean: 51.766 Å2 / Biso min: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1--4.2 Å2-0 Å22.35 Å2
2---2.88 Å2-0 Å2
3---5.43 Å2
Refinement stepCycle: final / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 74 9 2845
Biso mean--48.66 37.21 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172717
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.6523869
X-RAY DIFFRACTIONr_angle_other_deg1.0551.5956282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42122.025158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5381522
X-RAY DIFFRACTIONr_chiral_restr0.0370.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 40 -
Rwork0.369 758 -
all-798 -
obs--89.46 %
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)
11.3957-0.1293-0.03060.16210.05891.46160.03510.0502-0.0739-0.0102-0.04670.0389-0.044-0.0150.01160.1501-0.0085-0.09270.1421-0.00030.065-21.0637-2.4888-47.1387
20.8984-0.11740.29911.2544-0.76280.81830.01230.03690.0770.0550.0677-0.02470.1244-0.0231-0.080.14160.0021-0.07990.18890.00190.0577-11.8933-17.9199-20.3822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 902
2X-RAY DIFFRACTION2B6 - 902

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