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- PDB-2m55: NMR structure of the complex of an N-terminally acetylated alpha-... -

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Basic information

Entry
Database: PDB / ID: 2m55
TitleNMR structure of the complex of an N-terminally acetylated alpha-synuclein peptide with calmodulin
Components
  • Alpha-synuclein
  • Calmodulin
KeywordsCALCIUM BINDING PROTEIN/PROTEIN FIBRIL / Protein/peptide / Ca-binding / CALCIUM BINDING PROTEIN-PROTEIN FIBRIL complex
Function / homology
Function and homology information


: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / CaM pathway / regulation of glutamate secretion / Cam-PDE 1 activation / Sodium/Calcium exchangers / response to iron(II) ion / regulation of norepinephrine uptake / Calmodulin induced events / SNARE complex assembly / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / positive regulation of neurotransmitter secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / dopamine biosynthetic process / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / CaMK IV-mediated phosphorylation of CREB / regulation of synaptic vesicle exocytosis / Glycogen breakdown (glycogenolysis) / synaptic vesicle priming / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of macrophage activation / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / negative regulation of microtubule polymerization / CLEC7A (Dectin-1) induces NFAT activation / response to corticosterone / autophagosome membrane docking / synaptic vesicle transport / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / dynein complex binding / dopamine uptake involved in synaptic transmission / positive regulation of receptor recycling / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of dopamine secretion / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / protein kinase inhibitor activity / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of thrombin-activated receptor signaling pathway / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / response to type II interferon / cuprous ion binding / protein phosphatase activator activity / response to magnesium ion / RHO GTPases activate PAKs / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / Ion transport by P-type ATPases / : / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Uptake and function of anthrax toxins / Long-term potentiation / mitochondrial ATP synthesis coupled electron transport / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / synaptic vesicle endocytosis / catalytic complex / DARPP-32 events / regulation of presynapse assembly / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of serotonin uptake / Smooth Muscle Contraction
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein / : / 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 / Alpha-synuclein / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsGruschus, J.M. / Yap, T. / Pistolesi, S. / Maltsev, A.S. / Lee, J.C.
CitationJournal: Biochemistry / Year: 2013
Title: NMR Structure of Calmodulin Complexed to an N-Terminally Acetylated alpha-Synuclein Peptide.
Authors: Gruschus, J.M. / Yap, T.L. / Pistolesi, S. / Maltsev, A.S. / Lee, J.C.
History
DepositionFeb 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Source and taxonomy
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _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.pdbx_leaving_atom_flag / _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 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Alpha-synuclein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8616
Polymers18,7012
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 least restraint violations
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.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pet30b / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 1979.410 Da / Num. of mol.: 1 / Fragment: UNP residues 1-19 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P37840
#3: Chemical
ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-15N NOESY
1313D 1H-13C NOESY aliphatic
1412D 1H-13C HSQC aromatic
1523D 1H-13C NOESY aliphatic
1623D 1H-13C NOESY aromatic
1712D 1H-15N HSQC
1822D 1H-15N HSQC
1932D 1H-15N HSQC
11012D 1H-13C HSQC aliphatic
11112D 1H-13C HSQC aromatic
11222D 1H-13C HSQC aliphatic
11322D 1H-13C HSQC aromatic
11432D 1H-13C HSQC aliphatic
11513D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM [U-99% 13C; U-99% 15N] calmodulin, 600 uM alpha-synuclein, 50 mM MES, 100 mM potassium chloride, 3 mM calcium ion, 95% H2O/5% D2O95% H2O/5% D2O
2700 uM [U-13C; U-15N]-Met,Val,Phe,Gly,Leu,Ala alpha-synuclein, 700 uM calmodulin, 50 mM MES, 100 mM potassium chloride, 3 mM calcium ion, 0.1% sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
3150 uM [U-99% 13C; U-99% 15N] calmodulin, 150 uM alpha-synuclein, 50 mM MES, 100 mM potassium chloride, 3 mM calcium ion, 10 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMcalmodulin-1[U-99% 13C; U-99% 15N]1
600 uMalpha-synuclein-21
50 mMMES-31
100 mMpotassium chloride-41
3 mMCALCIUM ION-51
700 uMalpha-synuclein-6[U-13C; U-15N]-Met,Val,Phe,Gly,Leu,Ala2
700 uMcalmodulin-72
50 mMMES-82
100 mMpotassium chloride-92
3 mMCALCIUM ION-102
0.1 %sodium azide-112
150 uMcalmodulin-12[U-99% 13C; U-99% 15N]3
150 uMalpha-synuclein-133
50 mMMES-143
100 mMpotassium chloride-153
3 mMCALCIUM ION-163
10 mg/mLPf1 phage-173
Sample conditionspH: 6.36 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3467 / Protein phi angle constraints total count: 140 / Protein psi angle constraints total count: 140
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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