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- PDB-3tnf: LidA from Legionella in complex with active Rab8a -

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Basic information

Entry
Database: PDB / ID: 3tnf
TitleLidA from Legionella in complex with active Rab8a
Components
  • LidA
  • Ras-related protein Rab-8A
KeywordsPROTEIN TRANSPORT / vesicular trafficking / GTPase / Legionella pneumophila / Rab8a / vesicle recuitment / LCV / DrrA / SidM / Rab-effector / vesicular transport / GDP/GTP binding Rab-binding / ER / Golgi / Plasmamembrane
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 / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle ...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 / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle / regulation of exocytosis / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / non-motile cilium / endocytic recycling / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / cilium assembly / protein secretion / phagocytic vesicle / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / small monomeric GTPase / trans-Golgi network membrane / ciliary basal body / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / small GTPase binding / autophagy / 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 / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
LidA long coiled-coil domain / LidA long coiled-coil domain / Beta-Lactamase - #390 / Helix Hairpins - #2010 / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Helix Hairpins / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Beta-Lactamase / Rho (Ras homology) subfamily of Ras-like small GTPases ...LidA long coiled-coil domain / LidA long coiled-coil domain / Beta-Lactamase - #390 / Helix Hairpins - #2010 / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Helix Hairpins / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Beta-Lactamase / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Helix non-globular / Rab subfamily of small GTPases / Special / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-8A / LidA
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSchoebel, S. / Cichy, A.L. / Goody, R.S. / Itzen, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein LidA from Legionella is a Rab GTPase supereffector.
Authors: Schoebel, S. / Cichy, A.L. / Goody, R.S. / Itzen, A.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: LidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6698
Polymers64,6492
Non-polymers1,0196
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-74 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.820, 103.820, 150.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 20012.037 Da / Num. of mol.: 1 / Fragment: unp residues 6-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: synthetic DNASynthetic genomics / Gene: MEL, RAB8, RAB8A / Plasmid: pET19mod / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61006
#2: Protein LidA /


Mass: 44637.355 Da / Num. of mol.: 1 / Fragment: unp residues 201-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Legionella pneumophila subsp. pneumophila str. philadelphia 1
Gene: lida, lpg0940 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q5ZWZ3

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Non-polymers , 4 types, 68 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50% (v/v) MPD , 0.1 M sodium cacodylate pH 5.6, 10 mM spermidine, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9786
SYNCHROTRONSLS X10SA20.9786
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELMar 20, 2011
PSI PILATUS 6M2PIXELMar 20, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionNumber: 1133423 / Rmerge(I) obs: 0.12 / D res high: 3 Å / Num. obs: 31122 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
153021710010.038
101559710010.041
81079910010.047
68224710010.077
56284510010.096
4.55249110010.09
44.5392510010.114
3.54645310010.168
33.51152410010.39
ReflectionResolution: 2.5→30 Å / Num. obs: 29149 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.34
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.60.5934.591,299.5
2.6-2.70.3946.581,299.7
2.7-2.80.3028.121,299.7
2.8-2.90.21611.381,299.6
2.9-30.16814.511,299.9
3-3.50.08924.041,299.9
3.5-40.05240.251,2100
4-4.50.04448.251,2100
4.5-50.0450.311,2100
5-60.03649.71,2100
6-80.03353.961,2100
8-100.02854.981,299.8
10-150.02857.621,299.7
15-300.0356.211,299.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 2.03 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1458 5 %
Rwork0.216 --
obs0.2189 29141 99.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.522 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5077 Å20 Å2-0 Å2
2--6.5077 Å2-0 Å2
3----13.0154 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4463 0 65 62 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094592
X-RAY DIFFRACTIONf_angle_d1.0736156
X-RAY DIFFRACTIONf_dihedral_angle_d21.2881782
X-RAY DIFFRACTIONf_chiral_restr0.073666
X-RAY DIFFRACTIONf_plane_restr0.003785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.31451430.26622715X-RAY DIFFRACTION100
2.5894-2.6930.32991430.25792706X-RAY DIFFRACTION99
2.693-2.81560.34551430.27572724X-RAY DIFFRACTION100
2.8156-2.9640.38821430.27052719X-RAY DIFFRACTION100
2.964-3.14970.30551440.26322733X-RAY DIFFRACTION100
3.1497-3.39280.3231450.23462745X-RAY DIFFRACTION100
3.3928-3.73420.32351450.22652758X-RAY DIFFRACTION100
3.7342-4.27420.25691460.19162778X-RAY DIFFRACTION100
4.2742-5.3840.23171490.19012828X-RAY DIFFRACTION100
5.384-49.08620.23421570.20052977X-RAY DIFFRACTION100

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