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- PDB-2gzh: Crystal Structure of Rab11 in Complex with Rab11-Family Interacti... -

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Basic information

Entry
Database: PDB / ID: 2gzh
TitleCrystal Structure of Rab11 in Complex with Rab11-Family Interacting Protein 2
Components
  • RAB11-FIP2 long isoform
  • Ras-related protein Rab-11A
KeywordsPROTEIN 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 / plasma membrane to endosome transport / establishment of vesicle localization / 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 / plasma membrane to endosome transport / establishment of vesicle localization / 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 / phagocytic cup / mitotic metaphase chromosome alignment / establishment of cell polarity / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / mitotic spindle assembly / centriolar satellite / phagocytic vesicle / phagocytosis / transport vesicle / vesicle-mediated transport / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å
AuthorsKhan, A.R.
CitationJournal: Structure / Year: 2006
Title: Crystal structure of rab11 in complex with rab11 family interacting protein 2.
Authors: Jagoe, W.N. / Lindsay, A.J. / Read, R.J. / McCoy, A.J. / McCaffrey, M.W. / Khan, A.R.
History
DepositionMay 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 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_conn_type / 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-11A
B: RAB11-FIP2 long isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5516
Polymers31,8852
Non-polymers6674
Water2,252125
1
A: Ras-related protein Rab-11A
B: RAB11-FIP2 long isoform
hetero molecules

A: Ras-related protein Rab-11A
B: RAB11-FIP2 long isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10312
Polymers63,7694
Non-polymers1,3348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8980 Å2
ΔGint-103 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.740, 64.740, 112.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological unit is generated by the crystallographic 2-fold axis, transformation (1,-1,-1).

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 19547.830 Da / Num. of mol.: 1 / Fragment: G protein domain / Mutation: Q70L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11a / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62491, small monomeric GTPase
#2: Protein RAB11-FIP2 long isoform


Mass: 12336.811 Da / Num. of mol.: 1 / Fragment: Rab11-FIP2 Rab-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMAL-c2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7L804

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Non-polymers , 4 types, 129 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: Ammonium phosphate buffer, approximately 0.3M concentration, pH 5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98175 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2005
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98175 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. all: 10254 / Num. obs: 10234 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 16 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.3
Reflection shellResolution: 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
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.25353 492 4.8 %RANDOM
Rwork0.19655 ---
obs0.19914 9719 99.88 %-
all-10234 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refine analyzeLuzzati coordinate error free: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.47→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 39 125 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221889
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9872555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0965224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52623.29791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90315332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6561518
X-RAY DIFFRACTIONr_chiral_restr0.1170.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2560.2921
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21273
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2131.51152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14621806
X-RAY DIFFRACTIONr_scbond_it2.833843
X-RAY DIFFRACTIONr_scangle_it4.6314.5749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 43 -
Rwork0.222 684 -
obs--100 %

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