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- PDB-4c4p: Crystal Structure of Wild-Type Rab11 Complexed to FIP2 -

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Basic information

Entry
Database: PDB / ID: 4c4p
TitleCrystal Structure of Wild-Type Rab11 Complexed to FIP2
Components
  • RAB11 FAMILY-INTERACTING PROTEIN 2
  • RAS-RELATED PROTEIN RAB-11A
KeywordsPROTEIN TRANSPORT / EFFECTOR / VESICLE TRAFFICKING / ENDOSOMES
Function / homology
Function and homology information


TRAM-dependent toll-like receptor 4 signaling pathway / regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / exosomal secretion / regulated exocytosis / melanosome transport / astral microtubule organization ...TRAM-dependent toll-like receptor 4 signaling pathway / regulation of multivesicular body size / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / exosomal secretion / regulated exocytosis / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / amyloid-beta clearance by transcytosis / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / multivesicular body assembly / insulin secretion involved in cellular response to glucose stimulus / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / mitotic metaphase plate congression / phagocytic cup / syntaxin binding / positive regulation of epithelial cell migration / cleavage furrow / exocytosis / mitotic spindle assembly / centriolar satellite / phagocytosis / establishment of cell polarity / phagocytic vesicle / Vasopressin regulates renal water homeostasis via Aquaporins / G protein activity / transport vesicle / Anchoring of the basal body to the plasma membrane / small monomeric GTPase / positive regulation of G2/M transition of mitotic cell cycle / multivesicular body / centriole / vesicle-mediated transport / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of cytokinesis / cell projection / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / spindle pole / recycling endosome membrane / neuron projection development / positive regulation of GTPase activity / microtubule binding / cytoplasmic vesicle / vesicle / endosome / GTPase activity / axon / centrosome / glutamatergic synapse / intracellular membrane-bounded organelle / 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 / FIP-RBD domain profile. / FIP domain / FIP-RBD, C-terminal domain superfamily / Rab-binding domain FIP-RBD / 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 / FIP-RBD domain profile. / FIP domain / FIP-RBD, C-terminal domain superfamily / Rab-binding domain FIP-RBD / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-11A / Rab11 family-interacting protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsSultana, A. / Khan, A.R.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Structural and Functional Analysis of Fip2 Binding to the Endosome-Localised Rab25 Gtpase
Authors: Lall, P. / Horgan, C.P. / Oda, S. / Franklin, E. / Sultana, A. / Hanscomb, S.R. / Mccaffrey, M.W. / Khan, A.R.
History
DepositionSep 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Atomic model / Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Sep 16, 2015Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-11A
B: RAB11 FAMILY-INTERACTING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3524
Polymers31,8062
Non-polymers5472
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-6.4 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.560, 64.560, 112.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RAS-RELATED PROTEIN RAB-11A / RAB-11 / YL8


Mass: 19515.906 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62491
#2: Protein RAB11 FAMILY-INTERACTING PROTEIN 2 / RAB11-FIP2 / NRIP11


Mass: 12289.915 Da / Num. of mol.: 1 / Fragment: RAB-BINDING DOMAIN, RESIDUES 410-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7L804
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINALLY AND C-TERMINALLY TRUNCATED RAB11A, WITH A FEW NON-NATIVE RESIDUES AT N-TERMINUS FROM ...N-TERMINALLY AND C-TERMINALLY TRUNCATED RAB11A, WITH A FEW NON-NATIVE RESIDUES AT N-TERMINUS FROM CLONING SITE. FIP2 CONSISTS OF C-TERMINAL RAB-BINDING DOMAIN.

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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: 2.13 Å3/Da / Density % sol: 42.38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 18989 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.7

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→27.955 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 979 5.2 %
Rwork0.1804 --
obs0.1826 18980 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 33 176 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081939
X-RAY DIFFRACTIONf_angle_d1.0262646
X-RAY DIFFRACTIONf_dihedral_angle_d15.96747
X-RAY DIFFRACTIONf_chiral_restr0.051302
X-RAY DIFFRACTIONf_plane_restr0.003333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10560.23511430.19142513X-RAY DIFFRACTION100
2.1056-2.23740.2461370.17942537X-RAY DIFFRACTION100
2.2374-2.41010.22821360.17612534X-RAY DIFFRACTION100
2.4101-2.65250.22681410.17952545X-RAY DIFFRACTION100
2.6525-3.03590.23261450.18792552X-RAY DIFFRACTION100
3.0359-3.82330.22741450.17782596X-RAY DIFFRACTION100
3.8233-27.9580.2071320.1792724X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.9827 Å / Origin y: 8.3308 Å / Origin z: 21.774 Å
111213212223313233
T0.1469 Å20.0375 Å20.0252 Å2-0.1011 Å20.0069 Å2--0.1204 Å2
L1.1525 °2-0.2754 °20.0406 °2-1.5268 °2-0.4586 °2--1.2611 °2
S0.106 Å °0.0722 Å °0.204 Å °-0.2291 Å °0.0098 Å °-0.004 Å °-0.055 Å °-0.0813 Å °0.2179 Å °
Refinement TLS groupSelection details: ALL

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