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- PDB-3uct: Structure of Mn2+-bound N-terminal domain of calmodulin in the pr... -

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Basic information

Entry
Database: PDB / ID: 3uct
TitleStructure of Mn2+-bound N-terminal domain of calmodulin in the presence of Zn2+
ComponentsCalmodulin
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / METAL BINDING / CALCIUM REGULATION
Function / homology
Function and homology information


: / : / : / : / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / : / type 3 metabotropic glutamate receptor binding / positive regulation of peptidyl-threonine phosphorylation ...: / : / : / : / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / : / type 3 metabotropic glutamate receptor binding / positive regulation of peptidyl-threonine phosphorylation / positive regulation of DNA binding / CaM pathway / Cam-PDE 1 activation / positive regulation of protein serine/threonine kinase activity / 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 / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / response to corticosterone / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / regulation of synaptic vesicle exocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of calcium-mediated signaling / catalytic complex / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / activation of adenylate cyclase activity / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / positive regulation of nitric-oxide synthase activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / enzyme regulator activity / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / regulation of heart rate / Protein methylation / titin binding / response to amphetamine / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / positive regulation of receptor signaling pathway via JAK-STAT / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / spindle microtubule / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / G2/M transition of mitotic cell cycle / myelin sheath
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
: / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSenguen, F.T. / Grabarek, Z.
CitationJournal: Biochemistry / Year: 2012
Title: X-ray Structures of Magnesium and Manganese Complexes with the N-Terminal Domain of Calmodulin: Insights into the Mechanism and Specificity of Metal Ion Binding to an EF-Hand.
Authors: Senguen, F.T. / Grabarek, Z.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_dist_value / _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_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: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,19112
Polymers17,5992
Non-polymers59110
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Calmodulin
hetero molecules

B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,19112
Polymers17,5992
Non-polymers59110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area1390 Å2
ΔGint-134 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.288, 35.463, 58.343
Angle α, β, γ (deg.)90.000, 93.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin / CaM


Mass: 8799.724 Da / Num. of mol.: 2 / Fragment: N-terminal domain residues 2-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM, CALM1, CALM2, CALM3, CALML2, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII
Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100MM TRIS-CACODYLATE, 25MM ZNCL2, 16% PEG8000, 100MM MNCL2, 20% ETHYLENE GLYCOL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.758700, 1.075000
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2011 / Details: NINE QUADRANT
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.75871
21.0751
ReflectionRedundancy: 8.2 % / Number: 96889 / Rmerge(I) obs: 0.073 / Χ2: 1.38 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 11879 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095010010.0581.57410
3.254.0910010.0731.34610.8
2.843.2510010.0851.2849.3
2.582.8410010.0841.4537.4
2.392.5810010.1011.4897.4
2.252.3910010.1181.4937.4
2.142.2510010.1491.4527.3
2.052.1410010.21.3247.3
1.972.0510010.2651.2017.3
1.91.9799.910.3621.1687.2
ReflectionResolution: 1.9→58.257 Å / Num. all: 11882 / Num. obs: 11882 / % possible obs: 100 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 32.02 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALAdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→36.234 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.49 / σ(F): 1.94 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1088 4.77 %
Rwork0.202 --
obs0.2036 11882 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.14 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 76.17 Å2 / Biso mean: 39.7065 Å2 / Biso min: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.6449 Å2-0 Å25.5487 Å2
2---7.632 Å2-0 Å2
3---4.987 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 10 72 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171213
X-RAY DIFFRACTIONf_angle_d1.2181664
X-RAY DIFFRACTIONf_chiral_restr0.078177
X-RAY DIFFRACTIONf_plane_restr0.005211
X-RAY DIFFRACTIONf_dihedral_angle_d13.462445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.98650.29671320.23462670280298
1.9865-2.09120.26541600.241726942854100
2.0912-2.22220.27151260.217727262852100
2.2222-2.39380.25971410.204727232864100
2.3938-2.63460.29621250.219527442869100
2.6346-3.01570.2861430.223427092852100
3.0157-3.79880.21691210.202727362857100
3.7988-36.24090.18621400.176927202860100

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