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- PDB-3tkl: Crystal structure of the GTP-bound Rab1a in complex with the coil... -

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Basic information

Entry
Database: PDB / ID: 3tkl
TitleCrystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA from Legionella pneumophila
Components
  • LidA protein, substrate of the Dot/Icm system
  • Ras-related protein Rab-1A
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / Vesicle trafficking / PROTEIN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / COPII-coated vesicle cargo loading / RAB geranylgeranylation / melanosome transport / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / vesicle transport along microtubule / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / COPII-coated vesicle cargo loading / RAB geranylgeranylation / melanosome transport / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / vesicle transport along microtubule / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / endomembrane system / substrate adhesion-dependent cell spreading / small monomeric GTPase / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / G protein activity / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum / Golgi apparatus / extracellular exosome / cytosol
Similarity search - Function
Helix Hairpins - #990 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Helix Hairpins / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases ...Helix Hairpins - #990 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Helix Hairpins / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Special / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / Ras-related protein Rab-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 Å
AuthorsCheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural insights into a unique Legionella pneumophila effector LidA recognizing both GDP and GTP bound Rab1 in their active state
Authors: Cheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L.
History
DepositionAug 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: 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 / 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

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Assembly

Deposited unit
A: Ras-related protein Rab-1A
B: LidA protein, substrate of the Dot/Icm system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9494
Polymers52,4012
Non-polymers5472
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-23 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.823, 49.709, 61.702
Angle α, β, γ (deg.)90.00, 99.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 21766.635 Da / Num. of mol.: 1 / Fragment: UNP residues 1-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62820
#2: Protein LidA protein, substrate of the Dot/Icm system


Mass: 30634.645 Da / Num. of mol.: 1 / Fragment: Coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: lidA / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A5IFX1
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.86 Å3/Da / Density % sol: 33.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG3350, 0.7% butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 14, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.183→50 Å / Num. all: 20017 / Num. obs: 20017 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 25.74 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 23.88
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.65 / Num. unique all: 991 / Rsym value: 0.295 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FOL

2fol


Resolution: 2.183→31.785 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.35 / σ(I): 0 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1020 5.1 %RANDOM
Rwork0.1909 ---
all0.194 19986 --
obs0.194 19986 98.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.449 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 89.92 Å2 / Biso mean: 32.0164 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.5706 Å20 Å21.216 Å2
2---1.076 Å20 Å2
3---1.6466 Å2
Refinement stepCycle: LAST / Resolution: 2.183→31.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 33 111 3046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092980
X-RAY DIFFRACTIONf_angle_d1.0924015
X-RAY DIFFRACTIONf_chiral_restr0.068454
X-RAY DIFFRACTIONf_plane_restr0.004504
X-RAY DIFFRACTIONf_dihedral_angle_d17.2351156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1827-2.29780.28391270.20642537266492
2.2978-2.44170.27091350.196327152850100
2.4417-2.63010.31571590.209227142873100
2.6301-2.89470.26011460.216827422888100
2.8947-3.31310.29051500.193327522902100
3.3131-4.17270.21921470.175127502897100
4.1727-31.78880.21991560.18142756291298

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