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- PDB-3ucw: Structure of MG2+ bound N-Terminal domain of Calmodulin -

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Basic information

Entry
Database: PDB / ID: 3ucw
TitleStructure of MG2+ bound N-Terminal domain of Calmodulin
ComponentsCalmodulin
KeywordsCALCIUM-BINDING PROTEIN / EF-HAND / METAL BINDING / CALCIUM REGULATION
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 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.ptnr2_label_seq_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
C: Calmodulin
D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,44214
Polymers35,1994
Non-polymers24310
Water2,648147
1
A: Calmodulin
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7217
Polymers17,5992
Non-polymers1225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-47 kcal/mol
Surface area8390 Å2
MethodPISA
2
C: Calmodulin
hetero molecules

D: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7217
Polymers17,5992
Non-polymers1225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1860 Å2
ΔGint-46 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.435, 43.040, 53.689
Angle α, β, γ (deg.)68.44, 88.62, 79.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Calmodulin / CaM


Mass: 8799.724 Da / Num. of mol.: 4 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20MM TRIS CACODYLATE, 32% PEG8000, 25MM MGAC, 1MM EGTA, 50MM KCL, 25% ETHYLENE GLYCOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
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 wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 14.36 / Number: 107072 / Rmerge(I) obs: 0.071 / Χ2: 1.04 / D res high: 1.76 Å / D res low: 50 Å / Num. obs: 26501 / % possible obs: 95.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.795098.610.0580.6395.3
3.013.7997.810.070.735.5
2.633.0197.110.0750.9923.8
2.392.6397.210.0931.2733.8
2.222.3996.310.111.43.8
2.092.229610.1361.3423.8
1.982.0995.210.181.3473.8
1.91.9895.110.231.1753.7
1.821.994.810.3111.0283.6
1.761.8287.510.4040.8993.3
ReflectionResolution: 1.76→50 Å / Num. all: 27721 / Num. obs: 26501 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 28.433 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.042 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.76-1.823.30.40424060.899187.5
1.82-1.93.60.31126441.028194.8
1.9-1.983.70.2326421.175195.1
1.98-2.093.80.1826141.347195.2
2.09-2.223.80.13626901.342196
2.22-2.393.80.1126761.4196.3
2.39-2.633.80.09326911.273197.2
2.63-3.013.80.07526740.992197.1
3.01-3.795.50.0727400.73197.8
3.79-505.30.05827240.639198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å39.32 Å
Translation2.5 Å39.32 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→39.32 Å / Occupancy max: 1 / Occupancy min: 0.02 / SU ML: 0.49 / σ(F): 1.98 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1344 5.07 %
Rwork0.196 --
obs0.198 26491 94.82 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.376 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 91.39 Å2 / Biso mean: 36.3102 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1-6.0903 Å2-0.2483 Å23.2463 Å2
2---5.4939 Å20.1953 Å2
3----0.5964 Å2
Refinement stepCycle: LAST / Resolution: 1.76→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 10 147 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092506
X-RAY DIFFRACTIONf_angle_d0.8773441
X-RAY DIFFRACTIONf_chiral_restr0.051374
X-RAY DIFFRACTIONf_plane_restr0.004443
X-RAY DIFFRACTIONf_dihedral_angle_d16.85953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.8230.35491220.28072148227081
1.823-1.8960.25871220.242531265395
1.896-1.98230.28431190.21342521264095
1.9823-2.08680.25571300.20432520265095
2.0868-2.21760.26031420.20182548269096
2.2176-2.38880.231400.19072577271796
2.3888-2.62910.23571620.19682527268997
2.6291-3.00940.23381330.19062563269697
3.0094-3.79110.19221300.18472613274398
3.7911-39.33010.23661440.19282599274398

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