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- PDB-2q3x: The RIM1alpha C2B domain -

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Basic information

Entry
Database: PDB / ID: 2q3x
TitleThe RIM1alpha C2B domain
ComponentsRegulating synaptic membrane exocytosis protein 1
KeywordsTRANSPORT PROTEIN / C2 DOMAIN DIMER / NEUROTRANSMITTER RELEASE
Function / homology
Function and homology information


positive regulation of synaptic vesicle priming / positive regulation of synaptic vesicle fusion to presynaptic active zone membrane / extrinsic component of presynaptic active zone membrane / acrosomal vesicle exocytosis / regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / spontaneous neurotransmitter secretion / presynaptic dense core vesicle exocytosis / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle ...positive regulation of synaptic vesicle priming / positive regulation of synaptic vesicle fusion to presynaptic active zone membrane / extrinsic component of presynaptic active zone membrane / acrosomal vesicle exocytosis / regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / spontaneous neurotransmitter secretion / presynaptic dense core vesicle exocytosis / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / presynaptic active zone cytoplasmic component / inhibitory synapse / positive regulation of dendrite extension / positive regulation of inhibitory postsynaptic potential / neurotransmitter secretion / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / positive regulation of excitatory postsynaptic potential / regulation of membrane potential / cell projection / intracellular protein transport / regulation of long-term neuronal synaptic plasticity / GABA-ergic synapse / SH3 domain binding / small GTPase binding / long-term synaptic potentiation / presynaptic membrane / protein-containing complex assembly / vesicle / transmembrane transporter binding / cell differentiation / postsynaptic density / synapse / positive regulation of gene expression / protein kinase binding / glutamatergic synapse / zinc ion binding / plasma membrane
Similarity search - Function
: / RIM2-alpha zinc finger / Rim-like / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...: / RIM2-alpha zinc finger / Rim-like / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsGuan, R. / Dai, H. / Tomchick, D.R. / Machius, M. / Sudhof, T.C. / Rizo, J.
Citation
Journal: Biochemistry / Year: 2007
Title: Crystal Structure of the RIM1alpha C(2)B Domain at 1.7 A Resolution.
Authors: Guan, R. / Dai, H. / Tomchick, D.R. / Dulubova, I. / Machius, M. / Sudhof, T.C. / Rizo, J.
#1: Journal: Nature / Year: 2002
Title: RIM1alpha forms a protein scaffold for regulating neurotransmitter release at the active zone.
Authors: Schoch, S. / Castillo, P.E. / Jo, T. / Mukherjee, K. / Geppert, M. / Wang, Y. / Schmitz, F. / Malenka, R.C. / Sudhof, T.C.
#2: Journal: Nature / Year: 2002
Title: RIM1alpha is required for presynaptic long-term potentiation.
Authors: Castillo, P.E. / Schoch, S. / Schmitz, F. / Sudhof, T.C. / Malenka, R.C.
#3: Journal: Neuron / Year: 2004
Title: The presynaptic active zone protein RIM1alpha is critical for normal learning and memory.
Authors: Powell, C.M. / Schoch, S. / Monteggia, L. / Barrot, M. / Matos, M.F. / Feldmann, N. / Sudhof, T.C. / Nestler, E.J.
#4: Journal: Biochem.Soc.Trans. / Year: 2005
Title: RIM function in short- and long-term synaptic plasticity.
Authors: Kaeser, P.S. / Sudhof, T.C.
#5: Journal: J.Biol.Chem. / Year: 1998
Title: C2-domains, structure and function of a universal Ca2+-binding domain.
Authors: Rizo, J. / Sudhof, T.C.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Regulating synaptic membrane exocytosis protein 1
B: Regulating synaptic membrane exocytosis protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,71813
Polymers37,9162
Non-polymers80211
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-145 kcal/mol
Surface area12940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.037, 62.037, 145.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-184-

HOH

DetailsThe contents of the asymmetric unit is a homodimer.

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Components

#1: Protein Regulating synaptic membrane exocytosis protein 1 / Rab3-interacting molecule 1 / RIM 1


Mass: 18958.188 Da / Num. of mol.: 2 / Fragment: C2B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rims1, Rim1 / Plasmid: pGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9JIR4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1.9 M ammonium sulfate, 0.1 M sodium citrate, 0.15 M NaCl, 20% ethylene glycol, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.73→26.4 Å / Num. all: 34669 / Num. obs: 34669 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.73→1.775 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→26.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.82 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1400 4.1 %RANDOM
Rwork0.17784 ---
obs0.1793 33139 99.73 %-
all-33139 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.991 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.73→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 39 189 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222333
X-RAY DIFFRACTIONr_angle_refined_deg1.8112.0163170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0255292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56524.65186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69515423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4971512
X-RAY DIFFRACTIONr_chiral_restr0.1390.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021970
X-RAY DIFFRACTIONr_nbd_refined0.2060.21014
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.219
X-RAY DIFFRACTIONr_mcbond_it1.0481.51453
X-RAY DIFFRACTIONr_mcangle_it1.88922361
X-RAY DIFFRACTIONr_scbond_it2.8553910
X-RAY DIFFRACTIONr_scangle_it4.5254.5806
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 96 -
Rwork0.232 2423 -
obs-2519 99.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6496-0.09460.36370.7556-0.39481.36360.0204-0.02230.06140.0161-0.02010.0102-0.10210.0037-0.0004-0.0465-0.0083-0.0257-0.04610.027-0.037628.473422.502353.4834
21.64570.03430.31761.05810.02151.59180.1329-0.0638-0.15660.0751-0.0522-0.09220.14820.0188-0.0806-0.0189-0.0316-0.0523-0.06650.0351-0.044148.952715.166768.8056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1455 - 159411 - 150
2X-RAY DIFFRACTION2BB1455 - 159411 - 150

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