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- PDB-2cjt: Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Hetero... -

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Basic information

Entry
Database: PDB / ID: 2cjt
TitleStructural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules
ComponentsUNC-13 HOMOLOG A
KeywordsEXOCYTOSIS / PHORBOL-ESTER BINDING / NEUROTRANSMITTER RELEASE / RIM / MUNC13 / C2 DOMAINS / METAL-BINDING / PROTEIN-PROTEIN INTERACTIONS / ZINC FINGER / SYNAPTOSOME
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity / innervation / positive regulation of dendrite extension / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of amyloid precursor protein catabolic process / syntaxin-1 binding / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / spectrin binding / presynaptic active zone / synaptic vesicle exocytosis / calyx of Held / excitatory synapse / amyloid-beta metabolic process / SNARE binding / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / neuromuscular junction / terminal bouton / phospholipid binding / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / protein domain specific binding / axon / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein binding / plasma membrane
Similarity search - Function
Mammalian uncoordinated homology 13, domain 2 / Protein Unc-13 / Protein Unc-13, C2B domain / Munc13-homology domain 2 (MHD2) profile. / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / C2 domain ...Mammalian uncoordinated homology 13, domain 2 / Protein Unc-13 / Protein Unc-13, C2B domain / Munc13-homology domain 2 (MHD2) profile. / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Domain of Unknown Function (DUF1041) / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Protein unc-13 homolog A
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLu, J. / Machius, M. / Dulubova, I. / Dai, H. / Sudhof, T.C. / Tomchick, D.R. / Rizo, J.
Citation
Journal: Plos Biol. / Year: 2006
Title: Structural Basis for a Munc13-1 Dimeric 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: 2005
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
DepositionApr 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNC-13 HOMOLOG A
B: UNC-13 HOMOLOG A
C: UNC-13 HOMOLOG A
D: UNC-13 HOMOLOG A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,98138
Polymers59,0474
Non-polymers1,93434
Water11,548641
1
A: UNC-13 HOMOLOG A
C: UNC-13 HOMOLOG A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,52920
Polymers29,5242
Non-polymers1,00518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UNC-13 HOMOLOG A
D: UNC-13 HOMOLOG A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,45318
Polymers29,5242
Non-polymers92916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.558, 127.144, 50.739
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UNC-13 HOMOLOG A / MUNC13-1


Mass: 14761.839 Da / Num. of mol.: 4 / Fragment: C2A DOMAIN, RESIDUES 1-128
Source method: isolated from a genetically manipulated source
Details: THE RECOMBINANT PROTEIN CONTAINS RESIDUES 1-128 OF MUNC13-1 AND VECTOR-DERIVED SEQUENCES, GGV- AT THE N-TERMINUS
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q62768
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RECOMBINANT PROTEIN CONTAINS RESIDUES 1-128 OF MUNC13- 1 AND VECTOR-DERIVED SEQUENCES, GGV- AT ...THE RECOMBINANT PROTEIN CONTAINS RESIDUES 1-128 OF MUNC13- 1 AND VECTOR-DERIVED SEQUENCES, GGV- AT THE N-TERMINUS

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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: 2.4 Å3/Da / Density % sol: 48.3 %
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 growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: VAPOR DIFFUSION; HANGING DROP; PROTEIN: 12 MG/ML MUNC13-1 IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4; RESERVOIR: 0.4 M MAGNESIUM FORMATE, 0.1 M SODIUM ACETATE (PH 4.5); DROP: 1 ...Details: VAPOR DIFFUSION; HANGING DROP; PROTEIN: 12 MG/ML MUNC13-1 IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4; RESERVOIR: 0.4 M MAGNESIUM FORMATE, 0.1 M SODIUM ACETATE (PH 4.5); DROP: 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR; TEMPERATURE: 20 DEGREES CELSIUS; CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF ABOUT 0.05 MM X 0.05 MM X 0.35 MM WITHIN 3 DAYS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97959
DetectorType: CUSTOM / Detector: CCD / Date: Oct 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.44→47.12 Å / Num. obs: 99080 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.1
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.984 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1463 1.5 %RANDOM
Rwork0.16 ---
obs0.16 97532 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.05 Å2
2--0.08 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.44→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 125 641 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224336
X-RAY DIFFRACTIONr_bond_other_d0.0020.023964
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9385837
X-RAY DIFFRACTIONr_angle_other_deg0.92139239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53424.868189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02315757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7011520
X-RAY DIFFRACTIONr_chiral_restr0.1240.02649
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024723
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02848
X-RAY DIFFRACTIONr_nbd_refined0.2420.2588
X-RAY DIFFRACTIONr_nbd_other0.1970.23874
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22004
X-RAY DIFFRACTIONr_nbtor_other0.0880.22665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.2151
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6121.53327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82624204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.89432048
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8414.51627
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: 1.44→1.48 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 113
Rwork0.195 6946
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)
11.1507-0.02580.4510.60080.10760.6211-0.0043-0.0838-0.03750.03350.00540.0022-0.0128-0.0797-0.0011-0.0440.00440.017-0.02350.009-0.06340.841927.31238.7769
20.98840.0818-0.33360.6042-0.11160.5211-0.023-0.07650.05570.02020.01950.01160.0110.05260.0035-0.04710.0038-0.0086-0.016-0.0086-0.057831.297237.690834.1448
31.7511-0.09640.29851.64120.07311.87860.07590.013-0.24520.1691-0.0434-0.06730.15450.0591-0.0326-0.00450.00240.0059-0.0674-0.00570.005312.5979.8984-1.74
41.742-0.2444-0.05211.5481-0.10971.6297-0.0187-0.03760.27720.16790.02850.0661-0.1718-0.0362-0.00980.0182-0.0111-0.0115-0.04870.0020.038819.918555.032523.7978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 128
2X-RAY DIFFRACTION2B-3 - 128
3X-RAY DIFFRACTION3C2 - 128
4X-RAY DIFFRACTION4D2 - 128

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