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- PDB-2bwq: Crystal Structure of the RIM2 C2A-domain at 1.4 angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 2bwq
TitleCrystal Structure of the RIM2 C2A-domain at 1.4 angstrom Resolution
ComponentsREGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2
KeywordsTRANSPORT PROTEIN / C2 DOMAIN / NEUROTRANSMITTER RELEASE
Function / homology
Function and homology information


regulation of calcium-dependent activation of synaptic vesicle fusion / maintenance of presynaptic active zone structure / structural constituent of presynaptic active zone / cytoskeleton of presynaptic active zone / positive regulation of inhibitory postsynaptic potential / spontaneous neurotransmitter secretion / synaptic vesicle docking / inhibitory synapse / calcium ion-regulated exocytosis of neurotransmitter / photoreceptor ribbon synapse ...regulation of calcium-dependent activation of synaptic vesicle fusion / maintenance of presynaptic active zone structure / structural constituent of presynaptic active zone / cytoskeleton of presynaptic active zone / positive regulation of inhibitory postsynaptic potential / spontaneous neurotransmitter secretion / synaptic vesicle docking / inhibitory synapse / calcium ion-regulated exocytosis of neurotransmitter / photoreceptor ribbon synapse / presynaptic active zone cytoplasmic component / calcium-ion regulated exocytosis / regulation of exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / insulin secretion / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / exocytosis / positive regulation of excitatory postsynaptic potential / GABA-ergic synapse / positive regulation of synaptic transmission / regulation of membrane potential / cell projection / establishment of localization in cell / intracellular protein transport / regulation of synaptic plasticity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / small GTPase binding / protein-macromolecule adaptor activity / presynaptic membrane / transmembrane transporter binding / cell differentiation / protein domain specific binding / glutamatergic synapse / protein-containing complex binding / positive regulation of gene expression / protein-containing complex / metal ion binding
Similarity search - Function
Rim-like / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) ...Rim-like / Rab-binding domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Regulating synaptic membrane exocytosis protein 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsDai, H. / Tomchick, D.R. / Garcia, J. / Sudhof, T.C. / Machius, M. / Rizo, J.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of the Rim2 C(2)A-Domain at 1.4 A Resolution.
Authors: Dai, H. / Tomchick, D.R. / Garcia, J. / Sudhof, T.C. / Machius, M. / Rizo, J.
History
DepositionJul 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7733
Polymers15,5811
Non-polymers1922
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)25.455, 44.807, 55.756
Angle α, β, γ (deg.)90.00, 103.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2 / RAB3-INTERACTING MOLECULE / 2RIM2 C2A DOMAIN


Mass: 15580.859 Da / Num. of mol.: 1 / Fragment: C2 DOMAIN, RESIDUES 725-853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JIS1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.8 Å3/Da / Density % sol: 29.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: RAT RIM2 C2A-DOMAIN (RESIDUES 722-859) DISSOLVED IN 20 MM MES (PH 6.0), 150 MM NACL AND 1 MM EDTA WAS CONCENTRATED TO 25 MG/ML AND CRYSTALLIZED IN 17.5% (W/V) PEG 4000, 0.2 M (NH4)2SO4, 0.1M ...Details: RAT RIM2 C2A-DOMAIN (RESIDUES 722-859) DISSOLVED IN 20 MM MES (PH 6.0), 150 MM NACL AND 1 MM EDTA WAS CONCENTRATED TO 25 MG/ML AND CRYSTALLIZED IN 17.5% (W/V) PEG 4000, 0.2 M (NH4)2SO4, 0.1M SODIUM ACETATE (PH 4.5) AT 20 DEGREES C USING THE HANGING-DROP VAPOR-DIFFUSION METHOD. CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF 0.05 X 0.05 X 0.1 MM WITHIN TWO DAYS. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO A SOLUTION OF 20% (W/V) PEG 4000, 0.15M NACL, 0.2 M (NH4)2SO4, 0.1M SODIUM ACETATE (PH 4.5) AND 15% (V/V) ETHYLENE GLYCOL, AND THEN FLASH-COOLED IN LIQUID PROPANE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00691
DetectorType: CUSTOM / Detector: CCD / Date: Aug 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00691 Å / Relative weight: 1
ReflectionResolution: 1.41→20.91 Å / Num. obs: 23283 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 52.9
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.2 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V27

1v27


Resolution: 1.41→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.046 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1383 5.9 %RANDOM
Rwork0.181 ---
obs0.183 21884 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20.12 Å2
2--0.41 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.41→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 10 110 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221161
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9621581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43323.15857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4391510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.2473
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2765
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.441.5679
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14721090
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2793550
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9074.5491
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.45 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 91
Rwork0.225 1529
Refinement TLS params.Method: refined / Origin x: 10.0173 Å / Origin y: -0.0973 Å / Origin z: 12.5825 Å
111213212223313233
T-0.0276 Å2-0.0037 Å2-0.0029 Å2--0.0377 Å20.0027 Å2---0.0252 Å2
L0.9361 °2-0.0319 °2-0.3179 °2-0.6428 °2-0.2647 °2--1.1983 °2
S0.0049 Å °0.0521 Å °-0.0541 Å °-0.0824 Å °-0.0061 Å °0.0008 Å °0.0113 Å °0.0564 Å °0.0011 Å °

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