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- PDB-3jza: Crystal structure of human Rab1b in complex with the GEF domain o... -

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Basic information

Entry
Database: PDB / ID: 3jza
TitleCrystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila
Components
  • Ras-related protein Rab-1B
  • Uncharacterized protein DrrA
KeywordsTRANSPORT PROTEIN / RabGDI / RabGEF / GDI / GEF / GDF / GDI displacement factor / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Prenylation / Protein transport
Function / homology
Function and homology information


: / protein guanylylation / positive regulation of glycoprotein metabolic process / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs ...: / protein guanylylation / positive regulation of glycoprotein metabolic process / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / host cell cytoplasmic vesicle / Golgi Cisternae Pericentriolar Stack Reorganization / phosphatidylinositol-4-phosphate binding / protein targeting to membrane / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / regulation of GTPase activity / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / host cell cytoplasmic vesicle membrane / intracellular protein transport / small GTPase binding / protein guanylyltransferase activity / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / extracellular region / ATP binding / membrane / cytosol
Similarity search - Function
Ferritin - #70 / 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 / ARF-like small GTPases; ARF, ADP-ribosylation factor ...Ferritin - #70 / 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 / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ferritin / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Multifunctional virulence effector protein DrrA / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSchoebel, S. / Oesterlin, L.K. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
Citation
Journal: Mol.Cell / Year: 2009
Title: RabGDI displacement by DrrA from Legionella is a consequence of its guanine nucleotide exchange activity.
Authors: Schoebel, S. / Oesterlin, L.K. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
#1: Journal: Science / Year: 2007
Title: A bifunctional bacterial protein links GDI displacement to Rab1 activation.
Authors: Machner, M.P. / Isberg, R.R.
#2: Journal: Nature / Year: 2007
Title: Legionella pneumophila proteins that regulate Rab1 membrane cycling.
Authors: Ingmundson, A. / Delprato, A. / Lambright, D.G. / Roy, C.R.
History
DepositionSep 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-1B
B: Uncharacterized protein DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8603
Polymers41,7662
Non-polymers951
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-8.8 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.756, 100.756, 146.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
DetailsBiological unit is the same as asymmetric unit.

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Components

#1: Protein Ras-related protein Rab-1B


Mass: 19752.369 Da / Num. of mol.: 1 / Fragment: UNP residues 3-174
Source method: isolated from a genetically manipulated source
Details: codon-optimized synthetic gene / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Plasmid: pET19mod_TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0U4
#2: Protein Uncharacterized protein DrrA


Mass: 22013.141 Da / Num. of mol.: 1 / Fragment: GEF domain: UNP residues 340-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / DSM 7513 / Gene: lpg2464 / Plasmid: pET19mod_TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q5ZSQ3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 0.1 M Sodium citrate, 35% v/v PEG 600, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 31.75 / Number: 485728 / Rmerge(I) obs: 0.09 / D res high: 2.8 Å / Num. obs: 21262 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
520363197.810.051
45359110010.067
3.54361010010.091
3.23.5337610010.134
33.2304310010.197
2.93188099.910.259
2.82.9213110010.315
ReflectionResolution: 1.8→30 Å / Num. obs: 40529 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.85 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.4564.7550095873197.1
1.9-20.2797.3446424778197.5
2-2.10.19210.3366913954197.7
2.1-2.20.1913.8317473269197.9
2.2-2.30.26216.6301622743198.1
2.3-2.50.26820538484264198.3
2.5-30.20227.51130606410198.5
3-3.50.10138.2687653316199
3.5-40.06546.5382041883199.2
4-50.05253.5376561899199.2
5-70.05153.3254491311199.3
7-100.03758.98888526199.4
10-150.02862.52821204198.6
15-250.02855.393578196.3
25-300.02952.28491100

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.8 Å / Lowest resolution: 14.97 Å / Power centric: 0 / Reflection acentric: 9447

IDR cullis acentricPower acentricReflection centric
ISO_1002193
ANO_10.5153.6320
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_19.71-14.9700133111
ISO_17.72-9.7100196112
ISO_16.6-7.7200252107
ISO_15.86-6.600290111
ISO_15.33-5.8600325107
ISO_14.92-5.3300363104
ISO_14.59-4.9200397109
ISO_14.32-4.5900429102
ISO_14.09-4.3200445113
ISO_13.89-4.0900490106
ISO_13.72-3.8900507104
ISO_13.57-3.7200540114
ISO_13.44-3.5700559105
ISO_13.32-3.4400583116
ISO_13.21-3.3200602108
ISO_13.12-3.2100619117
ISO_13.03-3.1200659112
ISO_12.95-3.0300661111
ISO_12.87-2.9500694105
ISO_12.8-2.8700703119
ANO_19.71-14.970.20912.781330
ANO_17.72-9.710.22411.911960
ANO_16.6-7.720.18813.8992520
ANO_15.86-6.60.20612.1562900
ANO_15.33-5.860.249.7713250
ANO_14.92-5.330.288.1653630
ANO_14.59-4.920.3186.5943970
ANO_14.32-4.590.3315.8634290
ANO_14.09-4.320.3385.5674450
ANO_13.89-4.090.4234.1064900
ANO_13.72-3.890.4263.615070
ANO_13.57-3.720.4823.0035400
ANO_13.44-3.570.5622.3935590
ANO_13.32-3.440.6051.9165830
ANO_13.21-3.320.6631.546020
ANO_13.12-3.210.7171.2986190
ANO_13.03-3.120.7631.0356590
ANO_12.95-3.030.8320.836610
ANO_12.87-2.950.870.686940
ANO_12.8-2.870.8780.6357030
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-30.714-11.821-3.752SE71.721
2-25.661-6.009-16.181SE72.781
3-15.273-12.753-19.969SE80.371
4-26.599-12.891-1.351SE73.971
5-15.8441.95-11.378SE100.11
6-28.243-36.478-19.192SE93.931
7-38.282-38.42-21.543SE108.251
8-46.656-17.526-1.106SE128.151
9-22.803-2.397-27.213SE112.641
10-30.314-37.581-6.767SE237.621
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 32911
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.39-10034.90.779509
6.53-8.39310.886513
5.56-6.53300.911586
4.92-5.56220.947669
4.46-4.9217.60.959728
4.11-4.4618.40.96803
3.83-4.1118.80.955841
3.6-3.8318.60.949905
3.41-3.619.40.937950
3.24-3.4119.60.93982
3.1-3.24210.9191053
2.98-3.121.70.9091071
2.86-2.9825.80.8831134
2.76-2.8628.90.8811162
2.67-2.7625.70.8871192
2.59-2.6727.30.8611227
2.52-2.5924.90.8721281
2.45-2.5225.20.8721307
2.39-2.45280.861342
2.33-2.3926.40.8711370
2.27-2.3330.90.8361398
2.22-2.2788.40.6261434
2.18-2.2290.30.6241466
2.13-2.1891.90.6171496
2.09-2.1389.60.5721510
2.05-2.0987.90.5581560
2.01-2.0592.70.5541579
1.95-2.0191.10.4222843

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
DM6.1phasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.8 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2005 4.9 %RANDOM
Rwork0.201 ---
obs0.202 40517 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.349 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å2-1.4 Å20 Å2
2---2.79 Å20 Å2
3---4.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 5 246 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222906
X-RAY DIFFRACTIONr_bond_other_d0.0010.021955
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9653935
X-RAY DIFFRACTIONr_angle_other_deg1.0534816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35425.397126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36415540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5831512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_mcbond_it1.2921.51816
X-RAY DIFFRACTIONr_mcbond_other0.4641.5738
X-RAY DIFFRACTIONr_mcangle_it2.06722928
X-RAY DIFFRACTIONr_scbond_it3.12331090
X-RAY DIFFRACTIONr_scangle_it4.7314.5999
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 131 -
Rwork0.254 2732 -
all-2863 -
obs--96.85 %
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)
10.8452-0.6708-0.56211.7970.67171.1294-0.0175-0.10080.08180.15750.01630.0257-0.09820.00750.00120.08180.0278-0.02780.0934-0.06770.056119.0639-7.558519.8279
22.43320.03220.74282.04230.391.5825-0.17390.26170.4915-0.20380.0109-0.0951-0.15870.21620.1630.0799-0.0315-0.05480.11370.05050.12428.9077-13.7315-0.5561
33.60590.084-0.51231.04310.00170.8958-0.1908-0.4787-0.2710.14270.00260.03420.20620.0410.18820.1820.04160.02290.197-0.03190.082624.8045-30.712420.9262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B340 - 462
2X-RAY DIFFRACTION2B463 - 532
3X-RAY DIFFRACTION3A4 - 151
4X-RAY DIFFRACTION3A157 - 173

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