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- PDB-3tso: Structure of the cancer associated Rab25 protein in complex with FIP2 -

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Basic information

Entry
Database: PDB / ID: 3tso
TitleStructure of the cancer associated Rab25 protein in complex with FIP2
Components
  • Rab11 family-interacting protein 2
  • Ras-related protein Rab-25
KeywordsPROTEIN TRANSPORT / Ras GTPase fold (Rab25) / vesicle trafficking / endosome
Function / homology
Function and homology information


pseudopodium organization / pseudopodium membrane / TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / regulation of vesicle-mediated transport / epithelial cell morphogenesis / RAB geranylgeranylation / myosin V binding / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity ...pseudopodium organization / pseudopodium membrane / TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / regulation of vesicle-mediated transport / epithelial cell morphogenesis / RAB geranylgeranylation / myosin V binding / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / positive regulation of epithelial cell migration / exocytosis / pseudopodium / phagocytic cup / phagocytosis / positive regulation of GTPase activity / cell projection / positive regulation of protein localization to plasma membrane / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / protein transport / cytoplasmic vesicle / endosome / intracellular membrane-bounded organelle / GTPase activity / positive regulation of cell population proliferation / GTP binding / protein kinase binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane
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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Small GTPase / Ras family / Rab subfamily of small GTPases / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / PHOSPHATE ION / Ras-related protein Rab-25 / Rab11 family-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOda, S. / Lall, P.Y. / McCaffrey, M.W. / Khan, A.R.
CitationJournal: TO BE PUBLISHED
Title: Structure of the cancer associated Rab25 protein in complex with FIP2
Authors: Oda, S. / Lall, P.Y. / McCaffrey, M.W. / Khan, A.R.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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_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-25
B: Ras-related protein Rab-25
C: Rab11 family-interacting protein 2
D: Rab11 family-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,28515
Polymers57,5414
Non-polymers1,74311
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-87 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.310, 64.210, 65.940
Angle α, β, γ (deg.)113.25, 107.24, 99.46
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-25 / CATX-8


Mass: 19931.574 Da / Num. of mol.: 2 / Fragment: UNP residues 7-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB25, CATX8 / Production host: Escherichia coli (E. coli) / References: UniProt: P57735
#2: Protein Rab11 family-interacting protein 2 / Rab11-FIP2 / NRip11


Mass: 8839.037 Da / Num. of mol.: 2 / Fragment: UNP residues 440-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11FIP2, KIAA0941 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L804

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Non-polymers , 5 types, 219 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% PEG8000, 0.1M Na/K phosphate pH 6.2, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 108856 / Num. obs: 50863 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2 / % possible all: 78.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.18 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.263 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2499 5.1 %RANDOM
Rwork0.199 ---
obs0.201 46358 89.6 %-
all-50863 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.04 Å2-0.01 Å2
2--0 Å2-0.03 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 106 208 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223742
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9975084
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7985450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74923.576165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72415652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8861528
X-RAY DIFFRACTIONr_chiral_restr0.1560.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022711
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.52234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11223627
X-RAY DIFFRACTIONr_scbond_it3.35531508
X-RAY DIFFRACTIONr_scangle_it5.1924.51457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 126 -
Rwork0.358 2200 -
obs--58.14 %

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