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- PDB-5ez5: Crystal structure of active Rab11A (S20V) in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5ez5
TitleCrystal structure of active Rab11A (S20V) in complex with GTP
ComponentsRas-related protein Rab-11A
KeywordsTRANSPORT PROTEIN / small g protein / p-loop / ras
Function / homology
Function and homology information


: / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / : / regulation of endocytic recycling / establishment of vesicle localization / establishment of protein localization to organelle / postsynaptic recycling endosome / regulation of protein transport / positive regulation of mitotic cytokinetic process ...: / regulation of protein localization to centrosome / synaptic vesicle endosomal processing / : / regulation of endocytic recycling / establishment of vesicle localization / establishment of protein localization to organelle / postsynaptic recycling endosome / regulation of protein transport / positive regulation of mitotic cytokinetic process / regulation of cilium assembly / amyloid-beta clearance by transcytosis / exosomal secretion / neurotransmitter receptor transport, endosome to postsynaptic membrane / presynaptic endosome / plasma membrane to endosome transport / VxPx cargo-targeting to cilium / regulation of vesicle-mediated transport / melanosome transport / protein localization to cilium / astral microtubule organization / RAB geranylgeranylation / myosin V binding / multivesicular body assembly / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / syntaxin binding / dynein light intermediate chain binding / centriolar satellite / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / mitotic metaphase chromosome alignment / regulation of long-term neuronal synaptic plasticity / positive regulation of G2/M transition of mitotic cell cycle / transport vesicle / multivesicular body / vesicle-mediated transport / phagocytic vesicle / centriole / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / protein localization to plasma membrane / trans-Golgi network membrane / regulation of cytokinesis / positive regulation of protein localization to plasma membrane / small monomeric GTPase / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / recycling endosome / Schaffer collateral - CA1 synapse / neuron projection development / recycling endosome membrane / phagocytic vesicle membrane / spindle pole / endocytic vesicle membrane / cilium / synaptic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / cytoplasmic vesicle / G protein activity / microtubule binding / vesicle / Golgi membrane / centrosome / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol
Similarity search - Function
: / Small GTPase Rab domain 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 ...: / Small GTPase Rab domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsShin, Y.-C. / Yoon, J.H. / Park, H.H.
CitationJournal: To Be Published
Title: Crystal structure of active Rab11A (S20V) in complex with GTP
Authors: Shin, Y.-C. / Yoon, J.H. / Park, H.H.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)39,0806
Polymers37,9852
Non-polymers1,0954
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-28 kcal/mol
Surface area16030 Å2
2
A: Ras-related protein Rab-11A
hetero molecules

B: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0806
Polymers37,9852
Non-polymers1,0954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area1320 Å2
ΔGint-4 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.111, 74.111, 149.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 18992.475 Da / Num. of mol.: 2 / Fragment: UNP residues 8-175 / Mutation: S20V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium chloride, Tris, Magnessium chloride

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15662 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 30.8

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementResolution: 2.4→41.34 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.873 / SU B: 11.027 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.471 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3038 782 5 %RANDOM
Rwork0.23713 ---
obs0.24033 14877 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.544 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 2.4→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 66 10 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.9733722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74223.115122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84915440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6461522
X-RAY DIFFRACTIONr_chiral_restr0.2620.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.971.51660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88522658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.80531072
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4674.51064
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 55 -
Rwork0.279 1076 -
obs--99.12 %

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