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- PDB-3l0i: Complex structure of SidM/DrrA with the wild type Rab1 -

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Basic information

Entry
Database: PDB / ID: 3l0i
TitleComplex structure of SidM/DrrA with the wild type Rab1
Components
  • DrrA
  • Ras-related protein Rab-1A
KeywordsPROTEIN BINDING/PROTEIN TRANSPORT / GEF-GDF-Rab complex / GTP-binding / guanine-nucleotide exchange factor / GDI-Displacement factor / Type IV effector protein from legionella / PROTEIN BINDING-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


: / protein guanylylation / positive regulation of glycoprotein metabolic process / growth hormone secretion / AMPylase activity / protein adenylyltransferase / protein adenylylation / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule ...: / protein guanylylation / positive regulation of glycoprotein metabolic process / growth hormone secretion / AMPylase activity / protein adenylyltransferase / protein adenylylation / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / host cell cytoplasmic vesicle / endocytic recycling / Golgi Cisternae Pericentriolar Stack Reorganization / phosphatidylinositol-4-phosphate binding / protein targeting to membrane / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / regulation of GTPase activity / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / positive regulation of interleukin-8 production / host cell cytoplasmic vesicle membrane / intracellular protein transport / small GTPase binding / autophagy / endocytosis / melanosome / cell migration / protein guanylyltransferase activity / early endosome / endosome membrane / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1520 / de novo design (two linked rop proteins) - #370 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1520 / de novo design (two linked rop proteins) - #370 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / de novo design (two linked rop proteins) / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Rab-1A / Multifunctional virulence effector protein DrrA / Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsZhu, Y. / Shao, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA
Authors: Zhu, Y. / Hu, L. / Zhou, Y. / Yao, Q. / Liu, L. / Shao, F.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DrrA
B: Ras-related protein Rab-1A
C: DrrA
D: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,88010
Polymers129,4244
Non-polymers4556
Water43224
1
A: DrrA
B: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9044
Polymers64,7122
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-15 kcal/mol
Surface area23440 Å2
MethodPISA
2
C: DrrA
D: Ras-related protein Rab-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9756
Polymers64,7122
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-13 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.808, 71.747, 146.911
Angle α, β, γ (deg.)90.000, 93.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DrrA / / SidM


Mass: 41817.344 Da / Num. of mol.: 2 / Fragment: GEF/GDF domain, residues 193-550
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: sidM / Plasmid: pGEX-6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q29ST3, UniProt: Q5ZSQ3*PLUS
#2: Protein Ras-related protein Rab-1A / YPT1-related protein / Rab1a


Mass: 22894.861 Da / Num. of mol.: 2 / Fragment: small GTPase domain, residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P62820
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.59 Å3/Da / Density % sol: 52.57 % / Mosaicity: 1.026 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.1M ammonium sulfate, 0.1M sodium citrate, 0.4M Li2SO4, 0.1M di-ammonium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 31071 / Num. obs: 30947 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.103 / Χ2: 2.199 / Net I/σ(I): 13.1
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.542 / Num. unique all: 1546 / Χ2: 1.733 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→34.94 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.825 / SU B: 30.901 / SU ML: 0.281 / SU R Cruickshank DPI: 0.357 / SU Rfree: 0.415 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3108 10.1 %RANDOM
Rwork0.226 ---
all0.262 30947 --
obs0.23 30890 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.84 Å2 / Biso mean: 35.744 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.8 Å2
2--2.39 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.85→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7658 0 22 24 7704
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.007
X-RAY DIFFRACTIONr_angle_refined_deg1.039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.038
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.069
X-RAY DIFFRACTIONr_chiral_restr0.07
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_mcbond_it0.447
X-RAY DIFFRACTIONr_mcangle_it
LS refinement shellResolution: 2.855→2.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 237 -
Rwork0.284 1973 -
all-2210 -
obs--96.97 %
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)
12.1358-1.4989-1.71921.06911.093510.5615-0.20930.5909-0.3310.0846-0.40520.17321.1716-1.48820.61450.3997-0.32020.22250.8211-0.06750.2601-3.053630.4786157.712
21.01-0.4643-2.68560.24721.163311.0042-0.2310.3486-0.01990.0409-0.1991-0.07120.284-0.89580.430.3181-0.13430.10710.67540.08130.21273.260734.0116150.1535
33.08080.7242-3.03210.3687-0.11656.2556-0.1793-0.2543-0.0794-0.03330.0930.01070.44840.02150.08630.2490.06670.01010.42760.08580.049924.258731.4947115.4182
47.25293.3964-2.57792.1855-2.36323.69680.913-1.10880.78830.7241-0.53680.3904-1.46260.3571-0.37620.8479-0.08620.18470.4506-0.21530.134630.091345.7819124.97
53.43083.32251.91364.4923-0.14327.10310.5525-1.6904-0.27480.1267-0.941-0.804-0.24690.02670.38850.2478-0.5730.17321.954-0.36870.353435.072340.8187126.6765
61.51380.30711.59669.9566-3.00619.52980.4546-0.1983-0.54520.9936-0.3272-1.03270.13851.687-0.12740.25760.0906-0.24691.41250.14250.285242.639535.5477139.1994
70.69430.7645-0.41327.3776-5.8249.3585-0.11450.2615-0.48230.8539-0.5838-0.5131-1.09732.53280.69830.3355-0.2532-0.06941.73420.02280.447146.717145.4525131.9615
82.80140.5331-0.9241.3836-0.6316.6268-0.11480.5302-0.2948-0.09970.0885-0.19530.1387-0.46120.02630.1163-0.0586-0.08880.2308-0.02260.17571.641634.33442.8536
95.06142.2332-4.32421.0996-1.49815.18380.1389-0.30850.0161-0.0285-0.15780.0039-0.43930.12910.01890.12880.0241-0.05230.21090.06390.233964.66434.9664.5184
100.9963-0.7317-0.47640.98220.52472.5878-0.1261-0.1997-0.05790.14430.1135-0.0950.08180.29140.01260.11670.0184-0.05150.14880.01250.210644.528530.717687.3335
110.48510.1317-0.18691.68240.63480.7267-0.038-0.049-0.00870.00480.0788-0.0513-0.0930.0437-0.04080.1561-0.0096-0.02950.08520.02770.188632.040836.511275.6912
121.9074-0.24680.62133.98764.28626.4269-0.1347-0.03660.1444-0.3047-0.03280.4001-0.376-0.18150.16750.1195-0.0243-0.10940.02860.01410.31821.140732.585868.5717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A210 - 265
2X-RAY DIFFRACTION2A268 - 399
3X-RAY DIFFRACTION3A400 - 534
4X-RAY DIFFRACTION4B3 - 43
5X-RAY DIFFRACTION5B44 - 94
6X-RAY DIFFRACTION6B95 - 138
7X-RAY DIFFRACTION7B140 - 176
8X-RAY DIFFRACTION8C209 - 316
9X-RAY DIFFRACTION9C317 - 388
10X-RAY DIFFRACTION10C389 - 532
11X-RAY DIFFRACTION11D3 - 105
12X-RAY DIFFRACTION12D106 - 176

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