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- PDB-1r2q: Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution -

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Basic information

Entry
Database: PDB / ID: 1r2q
TitleCrystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution
ComponentsRas-related protein Rab-5A
KeywordsPROTEIN TRANSPORT / RAB / GTPase / GNP / atomic resolution
Function / homology
Function and homology information


receptor internalization involved in canonical Wnt signaling pathway / regulation of endosome size / cytoplasmic side of early endosome membrane / postsynaptic early endosome / synaptic vesicle recycling / regulation of autophagosome assembly / : / modulation by host of viral process / amyloid-beta clearance by transcytosis / regulation of filopodium assembly ...receptor internalization involved in canonical Wnt signaling pathway / regulation of endosome size / cytoplasmic side of early endosome membrane / postsynaptic early endosome / synaptic vesicle recycling / regulation of autophagosome assembly / : / modulation by host of viral process / amyloid-beta clearance by transcytosis / regulation of filopodium assembly / RAB geranylgeranylation / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / positive regulation of exocytosis / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / axon terminus / endocytic vesicle / somatodendritic compartment / phagocytosis / phagocytic vesicle / Prevention of phagosomal-lysosomal fusion / G protein activity / small monomeric GTPase / ruffle / regulation of synaptic vesicle exocytosis / clathrin-coated endocytic vesicle membrane / regulation of long-term neuronal synaptic plasticity / intracellular protein transport / terminal bouton / GDP binding / phagocytic vesicle membrane / melanosome / endocytosis / Clathrin-mediated endocytosis / actin cytoskeleton / synaptic vesicle / Factors involved in megakaryocyte development and platelet production / early endosome membrane / endosome membrane / early endosome / endosome / GTPase activity / axon / membrane raft / intracellular membrane-bounded organelle / dendrite / neuronal cell body / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsTerzyan, S. / Zhu, G. / Li, G. / Zhang, X.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Refinement of the structure of human Rab5a GTPase domain at 1.05 A resolution.
Authors: Terzyan, S. / Zhu, G. / Li, G. / Zhang, X.C.
History
DepositionSep 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0879
Polymers18,9881
Non-polymers1,0998
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.727, 64.573, 66.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18987.572 Da / Num. of mol.: 1 / Fragment: GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A OR RAB5 / Plasmid: pet11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): bl21(de3) / References: UniProt: P20339
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.73 Å3/Da / Density % sol: 29.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, SODIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.05→29.02 Å / Num. all: 68904 / Num. obs: 68904 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.7
Reflection shellResolution: 1.05→1.07 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3050 / % possible all: 79

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1N6N
Resolution: 1.05→29.02 Å / Num. parameters: 15339 / Num. restraintsaints: 19888 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Refinement was carried against F2
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 2063 -Random
Rwork0.1239 ---
all0.125 68700 --
obs0.124 68700 95 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL., 91, 201-228 (1973).
Refine analyzeNum. disordered residues: 55 / Occupancy sum hydrogen: 1293 / Occupancy sum non hydrogen: 1593.9
Refinement stepCycle: LAST / Resolution: 1.05→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 69 213 1617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d0.036
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.068
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0.109

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