- PDB-2hv8: Crystal structure of GTP-bound Rab11 in complex with FIP3 -
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Basic information
Entry
Database: PDB / ID: 2hv8
Title
Crystal structure of GTP-bound Rab11 in complex with FIP3
Components
Rab11 family-interacting protein 3
Ras-related protein Rab-11A
Keywords
PROTEIN TRANSPORT / Rab11a / FIP3 / cytokinesis / recycling endosomes
Function / homology
Function and homology information
postsynaptic recycling endosome membrane / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization ...postsynaptic recycling endosome membrane / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / negative regulation of adiponectin secretion / regulation of cilium assembly / exosomal secretion / melanosome transport / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / positive regulation of cilium assembly / multivesicular body assembly / dynein light intermediate chain binding / protein localization to cilium / endocytic recycling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / intercellular bridge / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / endocytic vesicle / vesicle-mediated transport / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / 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 / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / small GTPase binding / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / protein-macromolecule adaptor activity / midbody / cytoplasmic vesicle / microtubule binding / vesicle / molecular adaptor activity / endosome / cell cycle / cell division / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / calcium ion binding / protein-containing complex binding / GTP binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytosol Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
METHOXYETHANE / GUANOSINE-5'-TRIPHOSPHATE / Rab11 family-interacting protein 3 / Ras-related protein Rab-11A Similarity search - Component
Biological species
Homo sapiens (human)
Method
X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
A: Ras-related protein Rab-11A D: Rab11 family-interacting protein 3 B: Ras-related protein Rab-11A E: Rab11 family-interacting protein 3 C: Ras-related protein Rab-11A F: Rab11 family-interacting protein 3 hetero molecules
B: Ras-related protein Rab-11A E: Rab11 family-interacting protein 3 C: Ras-related protein Rab-11A F: Rab11 family-interacting protein 3 hetero molecules
Resolution: 1.86→8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.013 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2369
3221
5.1 %
RANDOM
Rwork
0.2034
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-
-
obs
0.2051
60337
98.24 %
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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: 29.957 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.45 Å2
0 Å2
1.3 Å2
2-
-
0.27 Å2
0 Å2
3-
-
-
0.88 Å2
Refinement step
Cycle: LAST / Resolution: 1.86→8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5073
0
140
906
6119
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
5283
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
0.972
1.978
7188
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.846
5
651
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.644
23.319
232
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.026
15
857
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.837
15
44
X-RAY DIFFRACTION
r_chiral_restr
0.062
0.2
845
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
3876
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.176
0.2
2668
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.295
0.2
3691
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.105
0.2
812
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.027
0.2
2
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.162
0.2
98
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.124
0.2
115
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
0.411
1.5
3372
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.692
2
5198
X-RAY DIFFRACTION
r_scbond_it
0.973
3
2226
X-RAY DIFFRACTION
r_scangle_it
1.545
4.5
1990
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.857→1.903 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.406
217
-
Rwork
0.329
3863
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obs
-
-
89.18 %
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