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- PDB-1zbd: STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE O... -

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Basic information

Entry
Database: PDB / ID: 1zbd
TitleSTRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A
Components(RABPHILIN-3A) x 2
KeywordsG PROTEIN / EFFECTOR / RABCDR / SYNAPTIC EXOCYTOSIS / RAB PROTEIN / RAB3A / RABPHILIN
Function / homology
Function and homology information


GDP-dissociation inhibitor binding / evoked neurotransmitter secretion / acrosomal vesicle exocytosis / RAB GEFs exchange GTP for GDP on RABs / maintenance of presynaptic active zone structure / regulation of plasma membrane repair / positive regulation of regulated secretory pathway / regulation of synaptic vesicle fusion to presynaptic active zone membrane / regulation of presynaptic dense core granule exocytosis / RAB geranylgeranylation ...GDP-dissociation inhibitor binding / evoked neurotransmitter secretion / acrosomal vesicle exocytosis / RAB GEFs exchange GTP for GDP on RABs / maintenance of presynaptic active zone structure / regulation of plasma membrane repair / positive regulation of regulated secretory pathway / regulation of synaptic vesicle fusion to presynaptic active zone membrane / regulation of presynaptic dense core granule exocytosis / RAB geranylgeranylation / selenium binding / sensory perception of touch / Rab protein signal transduction / spontaneous neurotransmitter secretion / synaptic vesicle recycling / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / calcium-dependent activation of synaptic vesicle fusion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / regulation of synaptic vesicle priming / synaptic vesicle clustering / synaptic vesicle maturation / positive regulation of calcium ion-dependent exocytosis / regulation of exocytosis / GTP-dependent protein binding / cholinergic synapse / extrinsic component of synaptic vesicle membrane / calcium-ion regulated exocytosis / myosin V binding / neuromuscular synaptic transmission / lysosome localization / plasma membrane repair / inositol 1,4,5 trisphosphate binding / respiratory system process / calcium-dependent phospholipid binding / regulation of short-term neuronal synaptic plasticity / dendritic spine organization / regulation of NMDA receptor activity / insulin secretion / extrinsic component of membrane / Neutrophil degranulation / synaptic vesicle priming / synaptic vesicle transport / regulation of synaptic vesicle exocytosis / phosphate ion binding / regulation of dopamine secretion / exocytosis / ATPase activator activity / synaptic vesicle exocytosis / presynaptic active zone / response to electrical stimulus / phosphatidylinositol-4,5-bisphosphate binding / axonogenesis / acrosomal vesicle / secretory granule / small monomeric GTPase / post-embryonic development / mitochondrion organization / establishment of localization in cell / intracellular protein transport / lung development / terminal bouton / neuromuscular junction / phospholipid binding / small GTPase binding / synaptic vesicle membrane / synaptic vesicle / presynapse / ATPase binding / protein-macromolecule adaptor activity / dendritic spine / postsynaptic membrane / lysosome / postsynapse / neuron projection / endosome / axon / GTPase activity / synapse / calcium ion binding / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / protein-containing complex / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Rab3 / Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / : / Zinc finger, FYVE-related ...Rab3 / Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / : / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / small GTPase Rab1 family profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Small GTPase / Ras family / Rab subfamily of small GTPases / Zinc finger, FYVE/PHD-type / Small GTP-binding protein domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Rabphilin-3A / Ras-related protein Rab-3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsOstermeier, C. / Brunger, A.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A.
Authors: Ostermeier, C. / Brunger, A.T.
History
DepositionNov 6, 1998Processing site: BNL
Revision 1.0Apr 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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: RABPHILIN-3A
B: RABPHILIN-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7866
Polymers39,1082
Non-polymers6784
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-32 kcal/mol
Surface area16030 Å2
MethodPISA
2
A: RABPHILIN-3A
B: RABPHILIN-3A
hetero molecules

A: RABPHILIN-3A
B: RABPHILIN-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,57212
Polymers78,2154
Non-polymers1,3578
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10330 Å2
ΔGint-69 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.315, 95.619, 47.715
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein RABPHILIN-3A / RAS-RELATED PROTEIN RAB-3A


Mass: 23439.336 Da / Num. of mol.: 1 / Fragment: 19-217 / Mutation: Q81L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: NEURONS / Cellular location: SYNAPTIC VESICLES / Organ: BRAIN / Plasmid: PET28A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P63012
#2: Protein RABPHILIN-3A / RAS-RELATED PROTEIN RAB-3A


Mass: 15668.363 Da / Num. of mol.: 1 / Fragment: 40-170, EFFECTOR DOMAIN / Mutation: C108S
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH GUANOSINE-5'-TRIPHOSPHATE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: NEURONS / Cellular location: SYNAPTIC VESICLES / Organ: BRAIN / Plasmid: PET15B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P47709

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Non-polymers , 4 types, 50 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 52.62 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 12.5 % / Common name: erythrotol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789, 0.9793, 0.9879
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 31, 1998 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
30.98791
ReflectionResolution: 2.6→90 Å / Num. obs: 23889 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.049 / Net I/σ(I): 17.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 0.3 / Rsym value: 0.22 / % possible all: 97.8
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→90 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 174722 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2213 9.4 %RANDOM
Rwork0.226 ---
obs0.226 23478 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.72 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 51.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.16 Å20 Å2-1.62 Å2
2--1.18 Å20 Å2
3----7.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 35 46 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.521.5
X-RAY DIFFRACTIONc_mcangle_it8.82
X-RAY DIFFRACTIONc_scbond_it9.852
X-RAY DIFFRACTIONc_scangle_it12.392.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 336 8.9 %
Rwork0.294 3456 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3GTP.PAR
X-RAY DIFFRACTION4WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.233 / Rfactor Rfree: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.375 / Rfactor obs: 0.3

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