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- PDB-2hv8: Crystal structure of GTP-bound Rab11 in complex with FIP3 -

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Basic information

Entry
Database: PDB / ID: 2hv8
TitleCrystal structure of GTP-bound Rab11 in complex with FIP3
Components
  • Rab11 family-interacting protein 3
  • Ras-related protein Rab-11A
KeywordsPROTEIN TRANSPORT / Rab11a / FIP3 / cytokinesis / recycling endosomes
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / negative regulation of adiponectin secretion ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / establishment of protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / negative regulation of adiponectin secretion / 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 / positive regulation of cilium assembly / RAB geranylgeranylation / Golgi to plasma membrane protein transport / multivesicular body assembly / protein localization to cilium / endocytic recycling / 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 / endocytic vesicle / mitotic spindle assembly / intercellular bridge / 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 / regulation of cytokinesis / small monomeric GTPase / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / recycling endosome / small GTPase binding / centriolar satellite / recycling endosome membrane / spindle pole / neuron projection development / Vasopressin regulates renal water homeostasis via Aquaporins / endocytic vesicle membrane / G protein activity / midbody / microtubule binding / cytoplasmic vesicle / protein-macromolecule adaptor activity / molecular adaptor activity / vesicle / endosome / ciliary basal body / cilium / Golgi membrane / cell division / GTPase activity / intracellular membrane-bounded organelle / centrosome / calcium ion binding / protein-containing complex binding / GTP binding / glutamatergic synapse / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / 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 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsEathiraj, S. / Mishra, A. / Prekeris, R. / Lambright, D.G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Rab11-mediated Recruitment of FIP3 to Recycling Endosomes.
Authors: Eathiraj, S. / Mishra, A. / Prekeris, R. / Lambright, D.G.
History
DepositionJul 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
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


Theoretical massNumber of molelcules
Total (without water)81,82119
Polymers79,4426
Non-polymers2,37813
Water16,322906
1
A: Ras-related protein Rab-11A
D: Rab11 family-interacting protein 3
hetero molecules

A: Ras-related protein Rab-11A
D: Rab11 family-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,24910
Polymers52,9624
Non-polymers1,2876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
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


Theoretical massNumber of molelcules
Total (without water)54,69614
Polymers52,9624
Non-polymers1,73510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-104 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.291, 52.601, 70.679
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-770-

HOH

21D-778-

HOH

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Components

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Protein , 2 types, 6 molecules ABCDEF

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


Mass: 19353.783 Da / Num. of mol.: 3 / Fragment: GTPase domain / Mutation: Q70L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIL / References: UniProt: P62491
#2: Protein Rab11 family-interacting protein 3 / Rab11-FIP3 / EF hands-containing Rab-interacting protein / Eferin


Mass: 7127.024 Da / Num. of mol.: 3 / Fragment: C-terminal region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11FIP3 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIL / References: UniProt: O75154

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Non-polymers , 6 types, 919 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-2ME / METHOXYETHANE


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 906 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG4000, 0.4M Ammonium Sulfate, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 18, 2005
RadiationMonochromator: CONFOCAL BLUE OPTIC DEVICE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 64429 / Num. obs: 64451 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.051 / Net I/σ(I): 27.5
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.259 / % possible all: 77

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1YZK

1yzk


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
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 3221 5.1 %RANDOM
Rwork0.2034 ---
obs0.2051 60337 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å21.3 Å2
2--0.27 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.86→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 140 906 6119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.9787188
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8465651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64423.319232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02615857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8371544
X-RAY DIFFRACTIONr_chiral_restr0.0620.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.22668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23691
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2812
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.2115
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4111.53372
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69225198
X-RAY DIFFRACTIONr_scbond_it0.97332226
X-RAY DIFFRACTIONr_scangle_it1.5454.51990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.857→1.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 217 -
Rwork0.329 3863 -
obs--89.18 %

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