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

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Basic information

Entry
Database: PDB / ID: 2cjs
TitleStructural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules
Components
  • REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2
  • UNC-13 HOMOLOG A
KeywordsEXOCYTOSIS / 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 information


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 / positive regulation of synaptic plasticity / synaptic vesicle docking ...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 / positive regulation of synaptic plasticity / synaptic vesicle docking / regulation of synaptic vesicle priming / photoreceptor ribbon synapse / 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 / syntaxin-1 binding / insulin secretion / 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 / intracellular protein transport / neuromuscular junction / establishment of localization in cell / phospholipid binding / GABA-ergic synapse / 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
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #120 / : / RIM2-alpha zinc finger / Rim-like / 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 ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #120 / : / RIM2-alpha zinc finger / Rim-like / 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) / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / 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 / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein unc-13 homolog A / Regulating synaptic membrane exocytosis protein 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 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: 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 1.2Jan 30, 2013Group: Database references / Derived calculations ...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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,00516
Polymers44,0113
Non-polymers99413
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-11.6 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.248, 93.534, 113.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 3 molecules ABC

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


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.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q62768
#2: Protein REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2 / RIM2ALPHA / RAB3-INTERACTING MOLECULE 2 / RIM 2


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.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-KT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JIS1

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Non-polymers , 4 types, 353 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsPLAYS A ROLE IN VESICLE MATURATION DURING EXOCYTOSIS AS A TARGET OF THE DIACYLGLYCEROL SECOND ...PLAYS A ROLE IN VESICLE MATURATION DURING EXOCYTOSIS AS A TARGET OF THE DIACYLGLYCEROL SECOND MESSENGER PATHWAY. RAB EFFECTOR INVOLVED IN EXOCYTOSIS ENGINEERED RESIDUE IN CHAIN A, LYS 32 TO GLU ENGINEERED RESIDUE IN CHAIN B, LYS 32 TO GLU
Sequence detailsTHE RECOMBINANT PROTEIN CONTAINS RESIDUES 2-150 OF MUNC13- 1 AND VECTOR-DERIVED SEQUENCES, ...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 AS WELL AS RESIDUES 83-142 OF RIM2S AND TWO VECTOR-DERIVED AMINO ACID RESIDUES, GS-, 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: 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 growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1593 3.1 %RANDOM
Rwork0.175 ---
obs0.176 50187 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--0.82 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 58 340 3347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9574448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1824.797148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5351519
X-RAY DIFFRACTIONr_chiral_restr0.1330.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022477
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21410
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22203
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2300
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3391.52043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98223225
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.89331432
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4314.51217
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: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 115 -
Rwork0.254 3657 -
obs--99.84 %
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)
12.99450.1941-0.71190.61990.02030.60050.05090.06730.1318-0.00650.0218-0.0077-0.05660.0115-0.0727-0.0340.01370.0025-0.07510.015-0.07591.02559.726716.3308
22.74010.19650.48031.1463-0.44661.9257-0.1257-0.5054-0.11160.20740.01550.0505-0.21750.0980.1102-0.02860.03010.0231-0.00310.0658-0.0845-1.4323-5.210340.8278
33.9974-0.5867-0.421.3445-0.21780.4962-0.0158-0.0097-0.11390.04130.01270.1452-0.005-0.04330.0031-0.06020.00710.0138-0.04610.0063-0.0313-18.32385.056422.9495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 154
2X-RAY DIFFRACTION2B-2 - 155
3X-RAY DIFFRACTION3C89 - 142

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