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- PDB-2cjs: Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Hetero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cjs | ||||||
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Title | Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules | ||||||
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![]() | EXOCYTOSIS / NEUROTRANSMITTER TRANSPORT / ZINC FINGER / SYNAPTOSOME / PHORBOL-ESTER BINDING / NEUROTRANSMITTER RELEASE / METAL-BINDING / PROTEIN- PROTEIN INTERACTIONS / RIM / MUNC13 / SYNAPSE / TRANSPORT / C2 DOMAINS | ||||||
Function / homology | ![]() regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / maintenance of presynaptic active zone structure / cytoskeleton of presynaptic active zone / dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / spontaneous neurotransmitter secretion / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis ...regulation of calcium-dependent activation of synaptic vesicle fusion / structural constituent of presynaptic active zone / maintenance of presynaptic active zone structure / cytoskeleton of presynaptic active zone / dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / spontaneous neurotransmitter secretion / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / inhibitory synapse / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity / photoreceptor ribbon synapse / calcium-ion regulated exocytosis / innervation / positive regulation of dendrite extension / regulation of exocytosis / positive regulation of inhibitory postsynaptic potential / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of amyloid precursor protein catabolic process / insulin secretion / syntaxin-1 binding / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / regulation of synaptic vesicle exocytosis / spectrin binding / exocytosis / presynaptic active zone / synaptic vesicle exocytosis / calyx of Held / positive regulation of excitatory postsynaptic potential / excitatory synapse / GABA-ergic synapse / amyloid-beta metabolic process / positive regulation of synaptic transmission / SNARE binding / synaptic membrane / synaptic transmission, glutamatergic / cell projection / establishment of localization in cell / regulation of membrane potential / long-term synaptic potentiation / intracellular protein transport / regulation of synaptic plasticity / neuromuscular junction / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / terminal bouton / phospholipid binding / synaptic vesicle membrane / small GTPase binding / presynapse / protein-macromolecule adaptor activity / presynaptic membrane / transmembrane transporter binding / cell differentiation / calmodulin binding / protein domain specific binding / axon / glutamatergic synapse / synapse / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / protein-containing complex / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, J. / Machius, M. / Dulubova, I. / Dai, H. / Sudhof, T.C. / Tomchick, D.R. / Rizo, J. | ||||||
![]() | ![]() Title: 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: ![]() Title: 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 |
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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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.6 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.1 KB | Display | ![]() |
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Full document | ![]() | 483.4 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 353 molecules ![](data/chem/img/EDO.gif)
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | PLAYS A ROLE IN VESICLE MATURATION DURING EXOCYTOSIS AS A TARGET OF THE DIACYLGLYCEROL SECOND ...PLAYS A ROLE IN VESICLE MATURATION |
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Sequence details | THE RECOMBINANT PROTEIN CONTAINS RESIDUES 2-150 OF MUNC13- 1 AND VECTOR-DERIVED SEQUENCES, ...THE RECOMBINAN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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. |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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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: 30.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→50 Å
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Refine LS restraints |
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