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- PDB-1yzk: GppNHp bound Rab11 GTPase -

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Basic information

Entry
Database: PDB / ID: 1yzk
TitleGppNHp bound Rab11 GTPase
ComponentsRas-related protein Rab-11A
KeywordsPROTEIN TRANSPORT / Rab GTPase / Rab11 / Vesicular trafficking
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of endocytic recycling / early endosome to recycling endosome transport / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / regulation of cilium assembly ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of endocytic recycling / early endosome to recycling endosome transport / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / melanosome transport / VxPx cargo-targeting to cilium / protein transmembrane transport / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane protein transport / multivesicular body assembly / protein localization to cilium / establishment of protein localization to membrane / syntaxin binding / protein localization to cell surface / TBC/RABGAPs / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / transport vesicle / vesicle-mediated transport / phagocytic vesicle / positive regulation of G2/M transition of mitotic cell cycle / multivesicular body / centriole / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / small monomeric GTPase / regulation of cytokinesis / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / recycling endosome / recycling endosome membrane / spindle pole / neuron projection development / Vasopressin regulates renal water homeostasis via Aquaporins / endocytic vesicle membrane / G protein activity / microtubule binding / cytoplasmic vesicle / vesicle / Golgi membrane / GTPase activity / centrosome / GTP binding / glutamatergic synapse / 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 ...: / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
CitationJournal: Nature / Year: 2005
Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 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 / 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 / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2993
Polymers20,7521
Non-polymers5472
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.946, 73.946, 148.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 20752.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P62491
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 54.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaCl, Glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2003
RadiationMonochromator: confocal blue optic device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14293 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.058 / Net I/σ(I): 31.6
Reflection shellResolution: 2→2.06 Å / Redundancy: 7 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 1139 / Rsym value: 0.252 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine Rab5c

Resolution: 2→6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.692 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22829 697 5.1 %RANDOM
Rwork0.17753 ---
all0.197 14295 --
obs0.18006 12992 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 33 219 1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221365
X-RAY DIFFRACTIONr_bond_other_d0.0010.021241
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.971859
X-RAY DIFFRACTIONr_angle_other_deg0.72332855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0123.11561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38115220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8491511
X-RAY DIFFRACTIONr_chiral_restr0.0560.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined0.20.2268
X-RAY DIFFRACTIONr_nbd_other0.170.21240
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2665
X-RAY DIFFRACTIONr_nbtor_other0.0770.2797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.51084
X-RAY DIFFRACTIONr_mcbond_other0.0811.5347
X-RAY DIFFRACTIONr_mcangle_it0.72321328
X-RAY DIFFRACTIONr_scbond_it1.1963644
X-RAY DIFFRACTIONr_scangle_it1.7824.5531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 45 -
Rwork0.234 837 -
obs--97.14 %

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