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- PDB-3rab: GPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 3rab
TitleGPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION
ComponentsPROTEIN (RAB3A)
KeywordsHYDROLASE / G PROTEIN / VESICULAR TRAFFICKING / GTP HYDROLYSIS / RAB PROTEIN / NEUROTRANSMITTER RELEASE
Function / homology
Function and homology information


GDP-dissociation inhibitor binding / evoked neurotransmitter secretion / acrosomal vesicle exocytosis / regulation of presynaptic dense core granule exocytosis / RAB GEFs exchange GTP for GDP on RABs / positive regulation of regulated secretory pathway / regulation of plasma membrane repair / maintenance of presynaptic active zone structure / regulation of synaptic vesicle fusion to presynaptic active zone membrane / sensory perception of touch ...GDP-dissociation inhibitor binding / evoked neurotransmitter secretion / acrosomal vesicle exocytosis / regulation of presynaptic dense core granule exocytosis / RAB GEFs exchange GTP for GDP on RABs / positive regulation of regulated secretory pathway / regulation of plasma membrane repair / maintenance of presynaptic active zone structure / regulation of synaptic vesicle fusion to presynaptic active zone membrane / sensory perception of touch / RAB geranylgeranylation / Rab protein signal transduction / synaptic vesicle recycling / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / synaptic vesicle clustering / neuromuscular synaptic transmission / synaptic vesicle maturation / GTP-dependent protein binding / respiratory system process / calcium-ion regulated exocytosis / myosin V binding / plasma membrane repair / lysosome localization / vesicle docking involved in exocytosis / regulation of exocytosis / regulation of short-term neuronal synaptic plasticity / insulin secretion / Neutrophil degranulation / synaptic vesicle transport / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / presynaptic active zone / exocytosis / synaptic vesicle exocytosis / ATPase activator activity / protein secretion / response to electrical stimulus / mitochondrion organization / axonogenesis / post-embryonic development / acrosomal vesicle / secretory granule / protein localization to plasma membrane / establishment of localization in cell / lung development / terminal bouton / synaptic vesicle membrane / synaptic vesicle / presynapse / protein-macromolecule adaptor activity / ATPase binding / postsynapse / lysosome / endosome / axon / GTPase activity / GTP binding / perinuclear region of cytoplasm / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Rab3 / 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Rab3 / 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 / Rab subfamily of small GTPases / 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-3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDumas, J.J. / Zhu, Z. / Connolly, J.L. / Lambright, D.G.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Structural basis of activation and GTP hydrolysis in Rab proteins.
Authors: Dumas, J.J. / Zhu, Z. / Connolly, J.L. / Lambright, D.G.
History
DepositionNov 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 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_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_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

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Assembly

Deposited unit
A: PROTEIN (RAB3A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2023
Polymers19,6551
Non-polymers5472
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.900, 35.000, 58.600
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (RAB3A)


Mass: 19655.135 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P63012
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.22 Å3/Da / Density % sol: 44 %
Crystal growpH: 6.5
Details: CRYSTALLIZATION CONDITIONS: 14%PEG-8000,50 MM NAMES, PH 6.5, 200 MM NACL
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
25 mMTris-HCl1drop
30.5 mM1dropMgCl2
414 %PEG80001reservoir
550 mMNaMES1reservoir
6200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 10595 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rsym value: 0.063 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 6.3 / Rsym value: 0.197 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.197

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5P21

5p21


Resolution: 2→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 -5 %RANDOM
Rwork0.191 ---
obs-10595 99.5 %-
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 33 123 1520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellHighest resolution: 2 Å /
Rfactor% reflection
Rfree0.23 -
Rwork0.184 -
obs-99.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor obs: 0.184

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