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- PDB-4d0g: Structure of Rab14 in complex with Rab-Coupling Protein (RCP) -

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Basic information

Entry
Database: PDB / ID: 4d0g
TitleStructure of Rab14 in complex with Rab-Coupling Protein (RCP)
Components
  • RAB11 FAMILY-INTERACTING PROTEIN 1
  • RAS-RELATED PROTEIN RAB-14
KeywordsHYDROLASE / RAB14 GTPASE / ENDOSOMAL TRAFFICKING / RAB- BINDING DOMAIN (RBD) / EFFECTOR RECRUITMENT
Function / homology
Function and homology information


phagolysosome assembly involved in apoptotic cell clearance / small GTPase binding => GO:0031267 / phagosome maturation / negative regulation of adiponectin secretion / Golgi to endosome transport / regulated exocytosis / RAB geranylgeranylation / myosin V binding / Golgi stack / trans-Golgi network transport vesicle ...phagolysosome assembly involved in apoptotic cell clearance / small GTPase binding => GO:0031267 / phagosome maturation / negative regulation of adiponectin secretion / Golgi to endosome transport / regulated exocytosis / RAB geranylgeranylation / myosin V binding / Golgi stack / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / nuclear outer membrane-endoplasmic reticulum membrane network / Synthesis of PIPs at the plasma membrane / tertiary granule membrane / regulation of embryonic development / intracellular transport / fibroblast growth factor receptor signaling pathway / endomembrane system / rough endoplasmic reticulum / vesicle-mediated transport / phagocytic vesicle / small monomeric GTPase / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / trans-Golgi network / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / regulation of protein localization / protein transport / late endosome / early endosome membrane / lysosome / early endosome / defense response to bacterium / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rab14 / 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) ...Ras-related protein Rab14 / 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
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-14 / Rab11 family-interacting protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLall, P. / Khan, A.R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure-Function Analyses of the Interactions between Rab11 and Rab14 Small Gtpases with Their Shared Effector Rab Coupling Protein (Rcp).
Authors: Lall, P. / Lindsay, A.J. / Hanscom, S. / Kecman, T. / Taglauer, E.S. / Mcveigh, U.M. / Franklin, E. / Mccaffrey, M.W. / Khan, A.R.
History
DepositionApr 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Aug 5, 2015Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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-14
C: RAB11 FAMILY-INTERACTING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3354
Polymers27,7882
Non-polymers5472
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-24.7 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.870, 148.228, 38.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RAS-RELATED PROTEIN RAB-14


Mass: 19773.424 Da / Num. of mol.: 1 / Fragment: RESIDUES 8-180 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61106
#2: Protein RAB11 FAMILY-INTERACTING PROTEIN 1 / RAB11-FIP1 / RAB-COUPLING PROTEIN


Mass: 8014.319 Da / Num. of mol.: 1 / Fragment: RESIDUES 582-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WKZ4
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*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


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNON-NATIVE RESIDUES AT N-TERMINUS DUE TO CLONING SITE. ALSO, SEVERAL RESIDUES HAVE FLEXIBLE SIDE ...NON-NATIVE RESIDUES AT N-TERMINUS DUE TO CLONING SITE. ALSO, SEVERAL RESIDUES HAVE FLEXIBLE SIDE CHAINS AND ARE MODELED AS ALANINE. FINALLY, THERE IS A SINGLE-SITE MUTATION (Q70L) IN RAB14. CHAIN C IS UNIPROT ISOFORM 3 Q6WKZ4-3.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.42 % / Description: NONE
Crystal growpH: 6.75 / Details: 14% PEG 8000, 0.1 M HEPES PH 6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9973 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.72 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DRZ

4drz


Resolution: 2.5→80.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.069 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. N- AND C-TERMINI ARE DISORDERED, AND SEVERAL SIDE-CHAINS ARE MODELED ALANINE DUE TO A LACK OF ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29438 960 9.9 %RANDOM
Rwork0.22403 ---
obs0.23113 8711 96.98 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→80.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 33 17 1706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191726
X-RAY DIFFRACTIONr_bond_other_d0.0010.021662
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9762346
X-RAY DIFFRACTIONr_angle_other_deg0.76433803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
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_it2.0924.251852
X-RAY DIFFRACTIONr_mcbond_other2.0834.246851
X-RAY DIFFRACTIONr_mcangle_it3.3936.3641062
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3044.453874
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 58 -
Rwork0.306 622 -
obs--92.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.804-1.28560.38964.5529-1.37672.6481-0.156-0.1030.03080.27050.2472-0.32510.12920.1012-0.09120.17310.0668-0.05120.0369-0.03850.0612-28.875-18.6425.381
22.22971.99410.755813.37872.40532.5552-0.26390.0052-0.197-0.56390.15050.25950.02810.02810.11350.06880.01160.02570.01970.01770.1056-46.34-29.439-10.977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 174
2X-RAY DIFFRACTION2C595 - 640

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