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- PDB-1z0f: GDP-Bound Rab14 GTPase -

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Basic information

Entry
Database: PDB / ID: 1z0f
TitleGDP-Bound Rab14 GTPase
ComponentsRAB14, member RAS oncogene family
KeywordsPROTEIN TRANSPORT / Rab GTPase / Rab14 / Vesicular trafficking
Function / homology
Function and homology information


phagolysosome assembly involved in apoptotic cell clearance / endosomal vesicle fusion / early endosome to Golgi transport / phagosome maturation / Golgi to endosome transport / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / Golgi stack / intracellular transport ...phagolysosome assembly involved in apoptotic cell clearance / endosomal vesicle fusion / early endosome to Golgi transport / phagosome maturation / Golgi to endosome transport / myosin V binding / RAB geranylgeranylation / trans-Golgi network transport vesicle / Golgi stack / intracellular transport / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / nuclear outer membrane-endoplasmic reticulum membrane network / Synthesis of PIPs at the plasma membrane / tertiary granule membrane / regulation of embryonic development / fibroblast growth factor receptor signaling pathway / endomembrane system / phagocytic vesicle / rough endoplasmic reticulum / vesicle-mediated transport / small monomeric GTPase / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / trans-Golgi network / recycling endosome / recycling endosome membrane / GDP binding / late endosome / regulation of protein localization / early endosome membrane / lysosome / early endosome / defense response to bacterium / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rab14 / : / 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 ...Ras-related protein Rab14 / : / 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-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionMar 1, 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 1.3Feb 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 1.4Apr 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: RAB14, member RAS oncogene family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5663
Polymers20,0991
Non-polymers4682
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.065, 40.780, 47.678
Angle α, β, γ (deg.)90.00, 108.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RAB14, member RAS oncogene family


Mass: 20098.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P61106
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.22 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7% PEG 6000, 100mM Calcium Chloride, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Mar 22, 2004 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 8450 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.122 / Net I/σ(I): 16.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 596 / Rsym value: 0.386 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine Rab4A

Resolution: 2.15→12 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.357 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.335 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 401 4.8 %RANDOM
Rwork0.20737 ---
all0.225 8469 --
obs0.20953 7998 97.38 %-
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: 28.305 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å21.55 Å2
2---0.82 Å20 Å2
3---3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.15→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 29 88 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9571770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71323.88954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65215192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.745157
X-RAY DIFFRACTIONr_chiral_restr0.0710.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02974
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.2524
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2880
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.5856
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75521301
X-RAY DIFFRACTIONr_scbond_it0.7973534
X-RAY DIFFRACTIONr_scangle_it1.2594.5469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 28 -
Rwork0.277 459 -
obs--82.82 %

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