- PDB-2ot3: Crystal structure of rabex-5 VPS9 domain in complex with nucleoti... -
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Basic information
Entry
Database: PDB / ID: 2ot3
Title
Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
Components
Rab5 GDP/GTP exchange factor
Ras-related protein Rab-21
Keywords
PROTEIN TRANSPORT / Rabex-5 / Vps9 Domain / Rab21 / vesicular traffic
Function / homology
Function and homology information
dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / cytoplasmic side of early endosome membrane / Kit signaling pathway / Rab protein signal transduction / negative regulation of mast cell degranulation / positive regulation of early endosome to late endosome transport / negative regulation of mast cell activation ...dendritic transport / negative regulation of Kit signaling pathway / mast cell migration / regulation of Fc receptor mediated stimulatory signaling pathway / cytoplasmic side of early endosome membrane / Kit signaling pathway / Rab protein signal transduction / negative regulation of mast cell degranulation / positive regulation of early endosome to late endosome transport / negative regulation of mast cell activation / negative regulation of leukocyte migration / negative regulation of receptor-mediated endocytosis / negative regulation of mast cell cytokine production / RAB geranylgeranylation / regulation of exocytosis / RAB GEFs exchange GTP for GDP on RABs / vesicle membrane / anterograde axonal transport / negative regulation of Ras protein signal transduction / TBC/RABGAPs / protein targeting to membrane / positive regulation of dendrite morphogenesis / regulation of axon extension / Golgi cisterna membrane / mast cell degranulation / negative regulation of interleukin-6 production / cleavage furrow / endocytic vesicle / endomembrane system / axon cytoplasm / guanyl-nucleotide exchange factor activity / receptor-mediated endocytosis / negative regulation of protein phosphorylation / intracellular protein transport / trans-Golgi network / recycling endosome / cytoplasmic side of plasma membrane / small GTPase binding / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / GDP binding / ubiquitin protein ligase activity / protein transport / early endosome membrane / Ras protein signal transduction / early endosome / protein stabilization / endosome / Golgi membrane / focal adhesion / GTPase activity / synapse / dendrite / endoplasmic reticulum membrane / nucleolus / GTP binding / DNA binding / zinc ion binding / extracellular exosome / cytosol Similarity search - Function
Rab21 / Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. ...Rab21 / Serum Albumin; Chain A, Domain 1 - #120 / VPS9 domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Serum Albumin; Chain A, Domain 1 / small GTPase Rab1 family profile. / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Type: ADSC QUANTUM 315 / Detector: CCD Details: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
Radiation
Monochromator: SI(11) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.642 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24272
1500
5.1 %
RANDOM
Rwork
0.18821
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-
-
obs
0.19099
28020
99.91 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 33.088 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.17 Å2
0 Å2
0 Å2
2-
-
-0.33 Å2
0 Å2
3-
-
-
1.5 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3179
0
0
463
3642
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
3234
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.23
1.965
4372
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.24
5
407
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.856
24.412
136
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.62
15
572
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.829
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.08
0.2
502
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2392
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.224
0.2
1761
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.304
0.2
2274
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.195
0.2
432
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.179
0.2
49
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.179
0.2
48
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.858
1.5
2105
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.486
2
3277
X-RAY DIFFRACTION
r_scbond_it
1.994
3
1285
X-RAY DIFFRACTION
r_scangle_it
3.211
4.5
1095
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.246
93
-
Rwork
0.208
2022
-
obs
-
-
100 %
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