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- PDB-1n6k: Crystal Structure of Human Rab5a A30P mutant complex with GDP and... -

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Basic information

Entry
Database: PDB / ID: 1n6k
TitleCrystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride
ComponentsRas-related protein Rab-5A
KeywordsPROTEIN TRANSPORT / Rab / GTPase
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 / anchored component of synaptic vesicle membrane / regulation of autophagosome assembly / amyloid-beta clearance by transcytosis / regulation of filopodium assembly / RAB geranylgeranylation ...receptor internalization involved in canonical Wnt signaling pathway / regulation of endosome size / cytoplasmic side of early endosome membrane / postsynaptic early endosome / synaptic vesicle recycling / anchored component of synaptic vesicle membrane / regulation of autophagosome assembly / 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 / axon terminus / regulation of endocytosis / endocytic vesicle / somatodendritic compartment / endomembrane system / phagocytosis / phagocytic vesicle / Prevention of phagosomal-lysosomal fusion / G protein activity / small monomeric GTPase / ruffle / intracellular protein transport / clathrin-coated endocytic vesicle membrane / regulation of long-term neuronal synaptic plasticity / regulation of synaptic vesicle exocytosis / GDP binding / terminal bouton / phagocytic vesicle membrane / melanosome / endocytosis / Clathrin-mediated endocytosis / actin cytoskeleton / synaptic vesicle / early endosome membrane / Factors involved in megakaryocyte development and platelet production / early endosome / endosome membrane / endosome / GTPase activity / viral RNA genome replication / axon / membrane raft / intracellular membrane-bounded organelle / neuronal cell body / GTP binding / dendrite / 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
ALUMINUM FLUORIDE / BETA-MERCAPTOETHANOL / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsZhu, G. / Liu, J. / Terzyan, S. / Zhai, P. / Li, G. / Zhang, X.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: High Resolution Crystal Structures of Human Rab5a and Five Mutants with Substitutions in the Catalytically Important Phosphate-Binding Loop
Authors: Zhu, G. / Liu, J. / Terzyan, S. / Zhai, P. / Li, G. / Zhang, X.C.
History
DepositionNov 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_conn.pdbx_dist_value ..._refine.ls_percent_reflns_obs / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6435
Polymers19,0141
Non-polymers6304
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)35.840, 64.040, 65.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ras-related protein Rab-5A / Rab5A


Mass: 19013.609 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN / Mutation: A30P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20339

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
35 mMGppNHp1drop
410 %(w/v)PEG60001reservoir
550-100 mMMES1reservoirpH6.0
60.2 M1reservoirNaCl
71 mM1reservoirMgCl2
80.1 %(v/v)beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 3, 2002
RadiationMonochromator: OSMIC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 22654 / Num. obs: 22063 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 31
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.7 / % possible all: 91.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 22654 / % possible obs: 99.8 % / Num. measured all: 116591
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1072 -RANDOM
Rwork0.177 ---
all0.18 22654 --
obs0.18 22062 97.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.388 Å20 Å20 Å2
2---1.39 Å20 Å2
3---0.002 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 37 250 1627
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_mcbond_it1.9231.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scangle_it3.5672
X-RAY DIFFRACTIONc_scbond_it4.8252.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gdp.paramgdp.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5bme1.parambme1.top
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2

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