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- PDB-2kdu: Structural basis of the Munc13-1/Ca2+-Calmodulin interaction: A n... -

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Basic information

Entry
Database: PDB / ID: 2kdu
TitleStructural basis of the Munc13-1/Ca2+-Calmodulin interaction: A novel 1-26 calmodulin binding motif with a bipartite binding mode
Components
  • Calmodulin
  • Protein unc-13 homolog A
KeywordsMETAL BINDING PROTEIN/EXOCYTOSIS / protein / calmodulin / Munc13 / calcium / Acetylation / Methylation / Alternative splicing / Cell junction / Cell membrane / Coiled coil / Cytoplasm / Exocytosis / Membrane / Metal-binding / Phorbol-ester binding / Phosphoprotein / Synapse / Zinc / Zinc-finger / METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX / METAL BINDING PROTEIN-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of glutamate receptor signaling pathway / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / synaptic vesicle maturation / positive regulation of glutamate receptor signaling pathway / 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 binding / syntaxin-1 binding / positive regulation of neurotransmitter secretion / 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 / enzyme regulator activity / SNARE binding / synaptic transmission, glutamatergic / synaptic membrane / 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 / signaling receptor binding / glutamatergic synapse / calcium ion binding / synapse / 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) / Phorbol esters/diacylglycerol binding domain (C1 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) / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 B / Protein unc-13 homolog A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing
AuthorsRodriguez-Castaneda, F.A. / Maestre-Martinez, M. / Coudevylle, N. / Dimova, K. / Jahn, O. / Junge, H. / Becker, S. / Brose, N. / Carlomagno, T. / Griesinger, C.
CitationJournal: Embo J. / Year: 2010
Title: Modular architecture of Munc13/calmodulin complexes: dual regulation by Ca2+ and possible function in short-term synaptic plasticity.
Authors: Rodriguez-Castaneda, F. / Maestre-Martinez, M. / Coudevylle, N. / Dimova, K. / Junge, H. / Lipstein, N. / Lee, D. / Becker, S. / Brose, N. / Jahn, O. / Carlomagno, T. / Griesinger, C.
History
DepositionJan 19, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin
B: Protein unc-13 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0586
Polymers20,8982
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1, calm2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62155, UniProt: P0DP33*PLUS
#2: Protein/peptide Protein unc-13 homolog A / Munc13-1


Mass: 4176.828 Da / Num. of mol.: 1 / Fragment: UNP residues 458-492, Calmodulin binding domain / Source method: obtained synthetically / References: UniProt: Q62768
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCO
1413D HN(CA)CO
1513D 1H-15N NOESY
1613D H(CCO)NH
1712D 1H-13C HSQC
1833D 1H-13C NOESY
1933D (H)CCH-TOCSY
11032D 1H-13C HSQC
11112D 1H-15N HSQC
11222D 1H-15N HSQC
11323D 1H-15N NOESY
11423D HNCO
11523D HN(CA)CO
11623D HN(CA)CB
11723D CBCA(CO)NH
11823D C(CO)NH
11923D H(CCO)NH
12023D (H)CCH-TOCSY
12113D C(CO)NH
12212D (IPAP)1H-15N HSQC
12322D (IPAP)1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM calcium, 1.5 mM [U-99% 13C; U-99% 15N] calmodulin, 1.8 mM Munc13-1, 150 mM potassium chloride, 20 mM BIS-TRIS, 90% H2O/10% D2O90% H2O/10% D2O
210 mM calcium, 0.5 mM [U-99% 13C; U-99% 15N] Munc13-1, 0.6 mM calmodulin, 150 mM potassium chloride, 20 mM BIS-TRIS, 90% H2O/10% D2O90% H2O/10% D2O
310 mM calcium, 1.5 mM [U-99% 13C; U-99% 15N] calmodulin, 1.8 mM Munc13, 150 mM potassium chloride, 20 mM BIS-TRIS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMcalcium-11
1.5 mMcalmodulin-2[U-99% 13C; U-99% 15N]1
1.8 mMMunc13-1-31
150 mMpotassium chloride-41
20 mMBIS-TRIS-51
10 mMcalcium-62
0.5 mMMunc13-1-7[U-99% 13C; U-99% 15N]2
0.6 mMcalmodulin-82
150 mMpotassium chloride-92
20 mMBIS-TRIS-102
10 mMcalcium-113
1.5 mMcalmodulin-12[U-99% 13C; U-99% 15N]3
1.8 mMMunc13-1-133
150 mMpotassium chloride-143
20 mMBIS-TRIS-153
Sample conditionspH: 6.8 / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9004
Bruker DMXBrukerDMX8005

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxdata analysis
FelixAccelrys Software Inc.processing
SparkyGoddardpeak picking
CANDIDHerrmann, Guntert and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Residual Dipolar Couplings refinement protocol
NMR constraintsNOE constraints total: 1647 / NOE intraresidue total count: 360 / NOE long range total count: 184 / NOE medium range total count: 557 / NOE sequential total count: 327
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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