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- PDB-1tu3: Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 1tu3
TitleCrystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain
Components
  • Rab GTPase binding effector protein 1
  • Ras-related protein Rab-5A
KeywordsPROTEIN TRANSPORT / Rab5 / Rabaptin5 / effector-binding
Function / homology
Function and homology information


regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of autophagosome assembly / Respiratory syncytial virus (RSV) attachment and entry / regulation of filopodium assembly ...regulation of endosome size / postsynaptic early endosome / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of autophagosome assembly / Respiratory syncytial virus (RSV) attachment and entry / regulation of filopodium assembly / Golgi to plasma membrane transport / RAB geranylgeranylation / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / endocytic vesicle / canonical Wnt signaling pathway / endomembrane system / phagocytosis / axon terminus / vesicle-mediated transport / phagocytic vesicle / Prevention of phagosomal-lysosomal fusion / somatodendritic compartment / ruffle / GTPase activator activity / small monomeric GTPase / G protein activity / regulation of long-term neuronal synaptic plasticity / intracellular protein transport / growth factor activity / clathrin-coated endocytic vesicle membrane / receptor internalization / terminal bouton / recycling endosome / endocytosis / phagocytic vesicle membrane / GDP binding / melanosome / actin cytoskeleton / synaptic vesicle / protein transport / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / early endosome membrane / membrane fusion / early endosome / endosome membrane / endosome / membrane raft / protein domain specific binding / axon / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / apoptotic process / dendrite / GTP binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / Single helix bin / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / Single helix bin / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-5A / Rab GTPase-binding effector protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis of Rab5-Rabaptin5 interaction in endocytosis
Authors: Zhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
E: Ras-related protein Rab-5A
F: Rab GTPase binding effector protein 1
G: Rab GTPase binding effector protein 1
H: Rab GTPase binding effector protein 1
I: Rab GTPase binding effector protein 1
J: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,70820
Polymers140,97510
Non-polymers2,73310
Water4,107228
1
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
F: Rab GTPase binding effector protein 1
G: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers56,3904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
H: Rab GTPase binding effector protein 1
I: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers56,3904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ras-related protein Rab-5A
J: Rab GTPase binding effector protein 1
hetero molecules

E: Ras-related protein Rab-5A
J: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers56,3904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)112.4, 83.5, 144.9
Angle α, β, γ (deg.)90.00, 102.2, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ras-related protein Rab-5A


Mass: 19118.766 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Plasmid: pET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20339
#2: Protein
Rab GTPase binding effector protein 1 / Rabaptin-5 / Rabaptin-5alpha / Rabaptin-4


Mass: 9076.241 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1, RABPT5, RABPT5A / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15276
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.4 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 54048 / Num. obs: 54048 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 89.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N6H

1n6h


Resolution: 2.31→29.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 423796.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1035 2 %RANDOM
Rwork0.222 ---
all0.222 51979 --
obs0.222 51979 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6721 Å2 / ksol: 0.304902 e/Å3
Displacement parametersBiso mean: 65.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.45 Å20 Å27.42 Å2
2---0.88 Å20 Å2
3----9.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.31→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 165 228 8735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.641.5
X-RAY DIFFRACTIONc_mcangle_it6.612
X-RAY DIFFRACTIONc_scbond_it6.852
X-RAY DIFFRACTIONc_scangle_it9.122.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.425 79 2.3 %
Rwork0.352 3321 -
obs--58.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GNP.PARGNP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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