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- PDB-3sfv: Crystal structure of the GDP-bound Rab1a S25N mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 3sfv
TitleCrystal structure of the GDP-bound Rab1a S25N mutant 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 / LidA-Rab Complex / Coiled-coil domain / Type IV effector protein from legionella / GDP Binding / 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
Beta-Lactamase - #390 / Helix Hairpins - #2010 / : / 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 / Beta-Lactamase / Helix non-globular / Rho (Ras homology) subfamily of Ras-like small GTPases ...Beta-Lactamase - #390 / Helix Hairpins - #2010 / : / 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 / Beta-Lactamase / Helix non-globular / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / Ras-related protein Rab-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsYin, K. / Lu, D. / Zhu, D. / Zhang, H. / Li, B. / Xu, S. / 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
DepositionJun 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 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 / 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 / _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-1A
B: LidA protein, substrate of the Dot/Icm system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1113
Polymers60,6682
Non-polymers4431
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-13 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.314, 54.673, 61.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20466.213 Da / Num. of mol.: 1 / Fragment: residues 1-176 / Mutation: S25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1A / Plasmid: pET15b / 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: 40201.562 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: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5IFX1
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 28% Jeffamin ED-2001, 0.1M sodium citrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 55418 / Num. obs: 55418 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 23
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 5.42 / Num. unique all: 5457 / Rsym value: 0.359 / % possible all: 100

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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 2FOL

2fol


Resolution: 1.73→50 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.18 / σ(F): 0 / σ(I): 0 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1918 3.6 %RANDOM
Rwork0.1918 ---
all0.1932 55418 --
obs0.1932 53216 95.99 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.134 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 62.88 Å2 / Biso mean: 24.07 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.6673 Å20 Å2-0 Å2
2--6.3512 Å2-0 Å2
3----4.684 Å2
Refinement stepCycle: LAST / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 28 389 4650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064344
X-RAY DIFFRACTIONf_angle_d0.965836
X-RAY DIFFRACTIONf_chiral_restr0.067637
X-RAY DIFFRACTIONf_plane_restr0.004742
X-RAY DIFFRACTIONf_dihedral_angle_d15.2081670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7296-1.77280.28031240.22733405352990
1.7728-1.82070.25181330.20913498363193
1.8207-1.87430.24511260.19783488361493
1.8743-1.93480.26421290.19683503363294
1.9348-2.00390.25521310.19313575370695
2.0039-2.08410.26491350.19533527366294
2.0841-2.1790.24141340.18523658379296
2.179-2.29380.21531410.18193694383597
2.2938-2.43740.22841400.1823675381597
2.4374-2.62550.22931430.1983746388998
2.6255-2.88940.25561410.20913766390798
2.8894-3.30690.22031440.20283825396999
3.3069-4.16410.18271440.173838904034100
4.1641-27.60560.23191530.191540484201100

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