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- PDB-1l7z: Crystal structure of Ca2+/Calmodulin complexed with myristoylated... -

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Basic information

Entry
Database: PDB / ID: 1l7z
TitleCrystal structure of Ca2+/Calmodulin complexed with myristoylated CAP-23/NAP-22 peptide
Components
  • CALMODULIN
  • CAP-23/NAP-22
KeywordsMETAL BINDING PROTEIN/PROTEIN BINDING / CALMODULIN / MYRISTOYLATION / PROTEIN-PROTEIN INTERACTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


: / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...: / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / negative regulation of peptidyl-threonine phosphorylation / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of peptidyl-threonine phosphorylation / positive regulation of ryanodine-sensitive calcium-release channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / positive regulation of DNA binding / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / response to corticosterone / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of ryanodine-sensitive calcium-release channel activity / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of protein autophosphorylation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / adenylate cyclase binding / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / presynaptic cytosol / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / positive regulation of nitric-oxide synthase activity / titin binding / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / voltage-gated potassium channel complex / regulation of calcium-mediated signaling / calcium channel complex / substantia nigra development / FCERI mediated Ca+2 mobilization / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / nitric-oxide synthase regulator activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / regulation of cytokinesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / mitochondrial membrane / cellular response to type II interferon
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / 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 ...EF-hand / : / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MYRISTIC ACID / : / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsubara, M. / Nakatsu, T. / Yamauchi, E. / Kato, H. / Taniguchi, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: EMBO J. / Year: 2004
Title: Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin
Authors: Matsubara, M. / Nakatsu, T. / Kato, H. / Taniguchi, H.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Identification of the calmodulin-binding domain of neuron-specific protein kinase C substrate protein CAP-22/NAP-22. Direct involvement of protein myristoylation in calmodulin-target protein interaction
Authors: Takasaki, A. / Hayashi, N. / Matsubara, M. / Yamauchi, E. / Taniguchi, H.
History
DepositionMar 18, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
B: CAP-23/NAP-22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0887
Polymers17,7002
Non-polymers3895
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.600, 40.600, 173.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACYC/hCaM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide CAP-23/NAP-22 / acidic membrane protein


Mass: 978.253 Da / Num. of mol.: 1 / Fragment: calmodulin binding domain / Source method: obtained synthetically / Details: synthetic myristoylated peptide / References: GenBank: 220820
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 1000, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.9 mMCaM1drop
22.7 mMpeptide1drop
310 mM1dropCaCl2
436 %PEG10001reservoir
520 mMcacodylate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 7, 2000
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 7815 / Num. obs: 7715 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 51.5 Å2 / Rsym value: 0.083 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.38 Å / Num. unique all: 793 / Rsym value: 0.192 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 7815 / Num. measured all: 39942 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QIV

1qiv


Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 408 -RANDOM
Rwork0.239 ---
all0.27 7685 --
obs0.249 7277 96.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 19 75 1231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.04
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.7
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 7799 / % reflection Rfree: 5 % / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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