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Open data
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Basic information
Entry | Database: PDB / ID: 2q3x | ||||||
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Title | The RIM1alpha C2B domain | ||||||
![]() | Regulating synaptic membrane exocytosis protein 1 | ||||||
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Function / homology | ![]() positive regulation of synaptic vesicle priming / positive regulation of synaptic vesicle fusion to presynaptic active zone membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guan, R. / Dai, H. / Tomchick, D.R. / Machius, M. / Sudhof, T.C. / Rizo, J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: RIM1alpha is required for presynaptic long-term potentiation. Authors: Castillo, P.E. / Schoch, S. / Schmitz, F. / Sudhof, T.C. / Malenka, R.C. #3: ![]() 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: ![]() Title: RIM function in short- and long-term synaptic plasticity. Authors: Kaeser, P.S. / Sudhof, T.C. #5: ![]() Title: C2-domains, structure and function of a universal Ca2+-binding domain. Authors: Rizo, J. / Sudhof, T.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.9 KB | Display | ![]() |
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PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The contents of the asymmetric unit is a homodimer. |
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Components
#1: Protein | Mass: 18958.188 Da / Num. of mol.: 2 / Fragment: C2B domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow![]() | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.991 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→26.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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