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- PDB-1nkf: CALCIUM-BINDING PEPTIDE, NMR, 30 STRUCTURES -

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Entry
Database: PDB / ID: 1nkf
TitleCALCIUM-BINDING PEPTIDE, NMR, 30 STRUCTURES
ComponentsCALCIUM-BINDING HEXADECAPEPTIDE
KeywordsCALCIUM-BINDING / EF HAND CALCIUM BINDING LOOP / ALPHA-HELIX
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / 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 synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium-mediated signaling / spindle microtubule / RAF activation
Similarity search - Function
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
LANTHANUM (III) ION / Calmodulin-1 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsSticht, H. / Ejchart, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Alpha-helix nucleation by a calcium-binding peptide loop.
Authors: Siedlecka, M. / Goch, G. / Ejchart, A. / Sticht, H. / Bierzyski, A.
History
DepositionMar 9, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM-BINDING HEXADECAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7462
Polymers1,6071
Non-polymers1391
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
RepresentativeModel #1

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Components

#1: Protein/peptide CALCIUM-BINDING HEXADECAPEPTIDE / CALMODULIN


Mass: 1606.649 Da / Num. of mol.: 1 / Mutation: D5N
Source method: isolated from a genetically manipulated source
Details: LA3+ ION BOUND / Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02593, UniProt: P0DP23*PLUS
#2: Chemical ChemComp-LA / LANTHANUM (III) ION / Lanthanum


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
1411H-13C-HMQC

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Sample preparation

DetailsContents: H2O/D2O(9:1)
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: 10E+5 PA atm / Temperature: 275.2 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
NDEEstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: DESCRIPTION OF THE STRATEGY USED FOR NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES ACCORDING TO THEIR INTENSITY: ...Details: DESCRIPTION OF THE STRATEGY USED FOR NMR STRUCTURE CALCULATION AND REFINEMENT: NOE CROSS-PEAKS WERE DIVIDED INTO THREE CATEGORIES AND ASSIGNED DISTANCE RANGES ACCORDING TO THEIR INTENSITY: STRONG, 0.18 - 0.27 NM; MEDIUM, 0.18 - 0.40 NM; WEAK, 0.18 - 0.55 NM. PEAK INTENSITIES WERE ESTIMATED FROM THE NUMBER OF CONTOURS IN NOESY SPECTRUM. HARMONIC RESTRAINTS FOR THE LA3+-ION WERE DEDUCED FROM THE POSITION OF THE CORRESPONDING CA2+-ION CRYSTAL STRUCTURE OF CALMODULIN (PDB CODE: 1CDM). A TOTAL OF SIX HARMONIC DISTANCE RESTRAINTS WAS INCLUDED IN ORDER TO FIX THE DISTANCE AND THE OCTAHEDRAL ARRANGEMENT OF THE SIX LIGANDS RELATIVE TO THE LA3+-ION ASSUMING THE SAME COORDINATION AS FOR THE CA2+ ION IN THE CALMODULIN CRYSTAL STRUCTURE. THE STRUCTURE CALCULATIONS USED THE AB INITIO SIMULATED ANNEALING (SA.INP) AND REFINEMENT (REFINE.INP) PROTOCOLS FROM THE X-PLOR PROGRAM PACKAGE. THE CALCULATIONS STARTED FROM AN EXTENDED TEMPLATE WITH RANDOMIZED BACKBONE TORSION ANGLES FOLLOWED BY 50 CYCLES OF ENERGY MINIMIZATION TO REMOVE CLOSE NON-BONDED CONTACTS. THE HIGH TEMPERATURE PHASE COMPRISED 50 PS OF DYNAMICS AT 1000 K; THE FINAL 16 PS HAD AN INCREASED WEIGHT ON COVALENT GEOMETRY RESTRAINTS AND THE NOE DERIVED DISTANCE RESTRAINTS. IN THE NEXT PHASE THE SYSTEM WAS SLOWLY COOLED FROM 1000 K TO 100 K IN A TIME OF 30 PS FOLLOWED BY 200 STEPS OF ENERGY MINIMIZATION. FOR THE NOE EFFECTIVE ENERGY TERM, REPRESENTING THE INTERPROTON DISTANCES, A SOFT SQUARE-WELL POTENTIAL WAS APPLIED. THE REFINEMENT PROTOCOL CONSISTED OF A SLOW-COOLING FROM 1000 TO 100 K WITHIN 45 PS. A FORCE CONSTANT OF 200 KCAL MOL-1 RAD-1 WAS USED FOR THE DIHEDRAL ANGLE RESTRAINTS WHILE THE NOE DERIVED DISTANCE RESTRAINTS AND HARMONIC RESTRAINT WERE REPRESENTED BY A SQUARE-WELL POTENTIAL FUNCTION WITH FORCE CONSTANT OF 50 KCAL/MOL1/A2. OF THE 200 RESULTING STRUCTURES, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST ENERGY AND THE LEAST VIOLATION OF THE EXPERIMENTAL DATA WERE SELECTED FOR FURTHER CHARACTERIZATION. GEOMETRY OF THE STRUCTURES AND ELEMENTS OF SECONDARY STRUCTURE WERE ANALYZED USING PROCHECK AND DSSP.
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 100 / Conformers submitted total number: 30

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