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- PDB-1oiv: X-ray structure of the small G protein Rab11a in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 1oiv
TitleX-ray structure of the small G protein Rab11a in complex with GDP
ComponentsRAS-RELATED PROTEIN RAB-11A
KeywordsPROTEIN TRANSPORT / SMALL G PROTEIN / INTRACELLULAR TRAFFICKING / GTP-BINDING / LIPOPROTEIN
Function / homology
Function and homology information


Anchoring of the basal body to the plasma membrane / VxPx cargo-targeting to cilium / RAB geranylgeranylation / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization ...Anchoring of the basal body to the plasma membrane / VxPx cargo-targeting to cilium / RAB geranylgeranylation / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome transport / kinetochore microtubule / astral microtubule organization / VxPx cargo-targeting to cilium / exocytic vesicle / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / protein localization to cilium / multivesicular body assembly / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / positive regulation of axon extension / vesicle-mediated transport / transport vesicle / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / endosome / protein domain specific binding / axon / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol
Similarity search - Function
small GTPase Rab1 family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase ...small GTPase Rab1 family profile. / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Structural Gdp/GTP Cycle of Rab11 Reveals a Novel Interface Involved in the Dynamics of Recycling Endosomes
Authors: Pasqualato, S. / Senic-Matuglia, F. / Renault, L. / Goud, B. / Salamero, J. / Cherfils, J.
History
DepositionJun 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-11A
B: RAS-RELATED PROTEIN RAB-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1256
Polymers43,0802
Non-polymers1,0454
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.349, 69.701, 108.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.31774, -0.90002, 0.29833), (-0.89605, 0.18213, -0.40487), (0.31005, -0.39596, -0.86434)
Vector: 2.64872, 5.48818, 10.76037)
DetailsTHIS MAY BE RESULT OF CRYSTAL PACKING

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Components

#1: Protein RAS-RELATED PROTEIN RAB-11A / RAB-11 / 24KG / YL8 / RAB11A


Mass: 21540.230 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-173
Source method: isolated from a genetically manipulated source
Details: DELETION MUTANT LACKING THE 43 C-TERMINAL RESIDUES / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24410, UniProt: P62491*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growpH: 8
Details: 1.7M (NH4)2SO4,5%PEG400,8% 1,3 BUTANEDIOL,0.1M TRIS-HCL PH8.0, pH 8.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 8.5 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.6-1.8 Mammonium sulfate1reservoir
33-6 %PEG4001reservoir
43-10 %1,3-butanediol1reservoir
5100 mMTris-HCl1reservoirpH8-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Nov 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 26143 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.393 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. obs: 26100 / Num. measured all: 233617 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G16

1g16


Resolution: 1.98→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1189171.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAP, AS WELL AS THE FIRST 5 RESIDUES OF RAB11A. ASP6 WAS MODELLED AS ALANINE BECAUSE ...Details: RESIDUES OF THE N-TERMINAL HIS6-TAG AND LINKER WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY MAP, AS WELL AS THE FIRST 5 RESIDUES OF RAB11A. ASP6 WAS MODELLED AS ALANINE BECAUSE ITS SIDE CHAIN WAS NOT VISIBLE
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1702 6.8 %RANDOM
Rwork0.21 ---
obs0.21 24954 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.7544 Å2 / ksol: 0.399156 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--3.31 Å20 Å2
3----3.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.98→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 65 191 2926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.12
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it4.262.5
LS refinement shellResolution: 1.98→2.03 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.272 103 6.2 %
Rwork0.239 1556 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP_XPLOR_PAR.TXTGDP_XPLOR_TOP.TXT
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EDO_XPLOR_PAR.TXTEDO_XPLOR_TOP.TXT
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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