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- PDB-3bya: Structure of a Calmodulin Complex -

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Basic information

Entry
Database: PDB / ID: 3bya
TitleStructure of a Calmodulin Complex
Components
  • Calmodulin
  • Glutamate [NMDA] receptor subunit zeta-1 peptide
KeywordsMETAL BINDING PROTEIN / Calmodulin / EF hand motif / NR1 / N-methyl-D-aspartate receptor / glutamate / central nervous system / neuronal channel / calcium channel / Methylation / Phosphoprotein / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Membrane / Postsynaptic cell membrane / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


excitatory chemical synaptic transmission / : / establishment of protein localization to mitochondrial membrane / Synaptic adhesion-like molecules / type 3 metabotropic glutamate receptor binding / propylene metabolic process / response to glycine / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity ...excitatory chemical synaptic transmission / : / establishment of protein localization to mitochondrial membrane / Synaptic adhesion-like molecules / type 3 metabotropic glutamate receptor binding / propylene metabolic process / response to glycine / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / NMDA selective glutamate receptor complex / Calmodulin induced events / calcium ion transmembrane import into cytosol / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / glutamate binding / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / protein heterotetramerization / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / regulation of synaptic vesicle exocytosis / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / positive regulation of calcium ion transport into cytosol / positive regulation of reactive oxygen species biosynthetic process / glycine binding / CLEC7A (Dectin-1) induces NFAT activation / response to corticosterone / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / monoatomic cation transmembrane transport / protein phosphatase activator activity / regulation of neuronal synaptic plasticity / RHO GTPases activate PAKs / monoatomic cation transport / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / excitatory synapse / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / ligand-gated monoatomic ion channel activity / positive regulation of excitatory postsynaptic potential / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / eNOS activation / Protein methylation / voltage-gated potassium channel complex / calcium ion homeostasis / activation of adenylate cyclase activity / enzyme regulator activity / synaptic cleft / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / glutamate-gated calcium ion channel activity / : / Ion homeostasis / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / EPHB-mediated forward signaling / nitric-oxide synthase regulator activity / substantia nigra development / adenylate cyclase activator activity
Similarity search - Function
: / : / : / EF-hand / Recoverin; domain 1 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...: / : / : / EF-hand / Recoverin; domain 1 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / EF-hand domain pair / Periplasmic binding protein-like I / 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
Calmodulin-1 / Calmodulin-3 / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBirrane, G. / Soni, A. / Ladias, J.A.A.
CitationJournal: To be Published
Title: Structure of a Calmodulin Complex
Authors: Birrane, G. / Soni, A. / Ladias, J.A.A.
History
DepositionJan 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Glutamate [NMDA] receptor subunit zeta-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6476
Polymers19,4872
Non-polymers1604
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.768, 42.737, 62.012
Angle α, β, γ (deg.)90.00, 106.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

21A-223-

HOH

DetailsThe biological assembly is the monomer contained in the asymmetric unit

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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 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Glutamate [NMDA] receptor subunit zeta-1 peptide / N-methyl-D-aspartate receptor subunit NR1


Mass: 2765.287 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide. The sequence is naturally found in human (homo sapiens).
References: UniProt: Q05586
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 17-19% PEG 3350, 0.120mM Ammonium Phosphate, 15% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2007 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 14639 / Num. obs: 14639 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.043 / Net I/σ(I): 28.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1457 / Rsym value: 0.332 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWQ

1iwq


Resolution: 1.85→32.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.438 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23159 735 5 %RANDOM
Rwork0.18125 ---
all0.18375 13948 --
obs0.18375 13948 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.04 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 4 79 1322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221288
X-RAY DIFFRACTIONr_bond_other_d0.0010.02879
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9671733
X-RAY DIFFRACTIONr_angle_other_deg0.99832156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59125.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49915251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.34158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined0.2410.2409
X-RAY DIFFRACTIONr_nbd_other0.1930.2937
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2660
X-RAY DIFFRACTIONr_nbtor_other0.0890.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1660.216
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2441.5832
X-RAY DIFFRACTIONr_mcbond_other0.321.5327
X-RAY DIFFRACTIONr_mcangle_it1.8121276
X-RAY DIFFRACTIONr_scbond_it3.0133520
X-RAY DIFFRACTIONr_scangle_it4.4854.5451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 62 -
Rwork0.199 1005 -
obs--98.98 %
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)
19.8289-3.0475-1.91081.8661-0.7023.4434-0.1775-2.21590.45140.36660.6046-0.1247-0.4048-0.1021-0.42720.11440.0949-0.02270.4711-0.0909-0.041623.413-4.03117.968
26.80190.11782.98555.21582.16277.41750.14150.034-0.1205-0.05120.0399-0.6263-0.26290.5229-0.1814-0.1420.0009-0.0237-0.147-0.01660.002317.198.6953.014
36.3081-3.2728-0.28632.32690.91491.8259-0.2787-0.6455-0.8690.18190.2580.35410.19460.11360.0206-0.10140.0250.0029-0.14340.0858-0.02086.5272.2897.041
416.4895-0.7201-2.93256.02091.0764.0023-0.1725-0.77660.70980.60350.3925-0.6681-0.4301-0.1298-0.220.04030.1197-0.0322-0.0773-0.0151-0.007518.8743.75311.934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 733 - 73
2X-RAY DIFFRACTION2AA81 - 9581 - 95
3X-RAY DIFFRACTION3AA96 - 14696 - 146
4X-RAY DIFFRACTION4BB875 - 8941 - 20

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