- PDB-2gzh: Crystal Structure of Rab11 in Complex with Rab11-Family Interacti... -
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Basic information
Entry
Database: PDB / ID: 2gzh
Title
Crystal Structure of Rab11 in Complex with Rab11-Family Interacting Protein 2
Components
RAB11-FIP2 long isoform
Ras-related protein Rab-11A
Keywords
PROTEIN TRANSPORT / Ras-like G protein fold / a-helical coiled coil
Function / homology
Function and homology information
TRAM-dependent toll-like receptor 4 signaling pathway / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly ...TRAM-dependent toll-like receptor 4 signaling pathway / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly / regulated exocytosis / exosomal secretion / amyloid-beta clearance by transcytosis / melanosome 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 / protein localization to cilium / multivesicular body assembly / dynein light intermediate chain binding / establishment of protein localization to membrane / protein localization to cell surface / insulin secretion involved in cellular response to glucose stimulus / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / establishment of cell polarity / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / phagocytic cup / centriolar satellite / mitotic spindle assembly / phagocytosis / vesicle-mediated transport / transport vesicle / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / cell projection / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / positive regulation of GTPase activity / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / endosome / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / protein kinase binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / cytosol Similarity search - Function
Rab11-family interacting protein class I / 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...Rab11-family interacting protein class I / 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Ras-related protein Rab-11A / Rab11 family-interacting protein 2 Similarity search - Component
Biological species
Homo sapiens (human)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å
Resolution: 2.47→2.56 Å / Redundancy: 10 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 15.9 / % possible all: 98.6
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
ADSC
datacollection
HKL-2000
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.47→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.799 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.29 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25353
492
4.8 %
RANDOM
Rwork
0.19655
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-
-
obs
0.19914
9719
99.88 %
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all
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10234
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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: 47.639 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.15 Å2
0.07 Å2
0 Å2
2-
-
0.15 Å2
0 Å2
3-
-
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-0.22 Å2
Refine analyze
Luzzati coordinate error free: 0.29 Å
Refinement step
Cycle: LAST / Resolution: 2.47→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1809
0
39
125
1973
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
1889
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.977
1.987
2555
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.096
5
224
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.526
23.297
91
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.903
15
332
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.656
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.117
0.2
290
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1393
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.256
0.2
921
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.317
0.2
1273
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.181
0.2
160
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
0.224
0.2
92
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.192
0.2
17
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
1.213
1.5
1152
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.146
2
1806
X-RAY DIFFRACTION
r_scbond_it
2.83
3
843
X-RAY DIFFRACTION
r_scangle_it
4.631
4.5
749
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.47→2.536 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.33
43
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Rwork
0.222
684
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obs
-
-
100 %
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