[English] 日本語
Yorodumi- PDB-2cjs: Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Hetero... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 2cjs | ||||||
|---|---|---|---|---|---|---|---|
| Title | Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules | ||||||
Components |
| ||||||
Keywords | EXOCYTOSIS / NEUROTRANSMITTER TRANSPORT / ZINC FINGER / SYNAPTOSOME / PHORBOL-ESTER BINDING / NEUROTRANSMITTER RELEASE / METAL-BINDING / PROTEIN- PROTEIN INTERACTIONS / RIM / MUNC13 / SYNAPSE / TRANSPORT / C2 DOMAINS | ||||||
| Function / homology | Function and homology informationregulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / spontaneous neurotransmitter secretion / calcium ion-regulated exocytosis of neurotransmitter / synaptic vesicle maturation / synaptic vesicle docking / regulation of synaptic vesicle priming ...regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / spontaneous neurotransmitter secretion / calcium ion-regulated exocytosis of neurotransmitter / synaptic vesicle maturation / synaptic vesicle docking / regulation of synaptic vesicle priming / photoreceptor ribbon synapse / positive regulation of synaptic plasticity / presynaptic active zone cytoplasmic component / inhibitory synapse / positive regulation of dendrite extension / regulation of exocytosis / calcium-ion regulated exocytosis / positive regulation of glutamate receptor signaling pathway / positive regulation of inhibitory postsynaptic potential / regulation of short-term neuronal synaptic plasticity / neurotransmitter secretion / innervation / regulation of amyloid precursor protein catabolic process / syntaxin binding / presynaptic active zone / insulin secretion / syntaxin-1 binding / Golgi-associated vesicle / positive regulation of neurotransmitter secretion / spectrin binding / neuromuscular junction development / synaptic vesicle priming / regulation of synaptic vesicle exocytosis / exocytosis / synaptic vesicle exocytosis / excitatory synapse / amyloid-beta metabolic process / positive regulation of excitatory postsynaptic potential / calyx of Held / synaptic membrane / SNARE binding / regulation of membrane potential / cell projection / synaptic transmission, glutamatergic / neuromuscular junction / intracellular protein transport / establishment of localization in cell / GABA-ergic synapse / phospholipid binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / small GTPase binding / long-term synaptic potentiation / terminal bouton / synaptic vesicle membrane / presynapse / presynaptic membrane / protein-macromolecule adaptor activity / transmembrane transporter binding / cell differentiation / calmodulin binding / protein domain specific binding / axon / calcium ion binding / synapse / positive regulation of gene expression / protein-containing complex binding / glutamatergic synapse / protein-containing complex / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Lu, J. / Machius, M. / Dulubova, I. / Dai, H. / Sudhof, T.C. / Tomchick, D.R. / Rizo, J. | ||||||
Citation | Journal: Plos Biol. / Year: 2006Title: Structural Basis for a Munc13-1 Homodimer to Munc13-1/Rim Heterodimer Switch. Authors: Lu, J. / Machius, M. / Dulubova, I. / Dai, H. / Sudhof, T.C. / Tomchick, D.R. / Rizo, J. #1: Journal: Embo J. / Year: 2005Title: A Munc13-Rim-Rab3 Tripartite Complex: From Priming to Plasticity Authors: Dulubova, I. / Lou, X. / Lu, J. / Huryeva, I. / Alam, A. / Schneggenburger, R. / Sudhof, T.T. / Rizo, J. | ||||||
| History |
| ||||||
| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 2cjs.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb2cjs.ent.gz | 79.1 KB | Display | PDB format |
| PDBx/mmJSON format | 2cjs.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2cjs_validation.pdf.gz | 474.1 KB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 2cjs_full_validation.pdf.gz | 483.4 KB | Display | |
| Data in XML | 2cjs_validation.xml.gz | 21.7 KB | Display | |
| Data in CIF | 2cjs_validation.cif.gz | 31 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cjs ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cjs | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 |
| ||||||||
| Unit cell |
|
-
Components
-Protein , 2 types, 3 molecules ABC
| #1: Protein | Mass: 18570.021 Da / Num. of mol.: 2 / Fragment: C2A DOMAIN, RESIDUES 2-150 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE RECOMBINANT PROTEIN CONTAINS RESIDUES 2-150 OF MUNC13-1 AND VECTOR-DERIVED SEQUENCES, GSPGISGGGGGIL- AT THE N-TERMINUS AND -KLNSS AT THE C- TERMINUS Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 6870.929 Da / Num. of mol.: 1 / Fragment: ZINC-FINGER DOMAIN, RESIDUES 83-142 Source method: isolated from a genetically manipulated source Details: THE RECOMBINANT PROTEIN CONTAINS RESIDUES 83-142 AND TWO VECTOR-DERIVED AMINO ACID RESIDUES, GS-, AT THE N TERMINUS Source: (gene. exp.) ![]() ![]() |
|---|
-Non-polymers , 4 types, 353 molecules 






| #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
|---|
-Details
| Compound details | PLAYS A ROLE IN VESICLE MATURATION DURING EXOCYTOSIS AS A TARGET OF THE DIACYLGLYCEROL SECOND ...PLAYS A ROLE IN VESICLE MATURATION |
|---|---|
| Sequence details | THE RECOMBINANT PROTEIN CONTAINS RESIDUES 2-150 OF MUNC13- 1 AND VECTOR-DERIVED SEQUENCES, ...THE RECOMBINAN |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.3 % Description: FOR MOLECULAR REPLACEMENT, INITIAL MODEL COORDINATES WERE OBTAINED BY MODIFYING THE COORDINATES OF THE RAT MUNC13-1 C2B-DOMAIN DERIVED FROM OUR UNPUBLISHED RESULTS. |
|---|---|
| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: VAPOR DIFFUSION; HANGING DROP; PROTEIN: 10 MG/ML MUNC13-1/RIM2ALPHA IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4); RESERVOIR: 0.3 M AMMONIUM TARTRATE (PH 7.0); DROP: 1 MICROLITER PROTEIN ...Details: VAPOR DIFFUSION; HANGING DROP; PROTEIN: 10 MG/ML MUNC13-1/RIM2ALPHA IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4); RESERVOIR: 0.3 M AMMONIUM TARTRATE (PH 7.0); DROP: 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR; TEMPERATURE: 20 DEGREES CELSIUS; CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF ABOUT 0.06 MM X 0.06 MM X 0.25 MM WITHIN 4 DAYS. |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 |
| Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 12, 2005 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
| Reflection | Resolution: 1.78→37.57 Å / Num. obs: 51718 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.1 |
| Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.227 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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: 30.79 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.78→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




X-RAY DIFFRACTION
Citation













PDBj







