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- PDB-4hex: A novel conformation of calmodulin -

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Basic information

Entry
Database: PDB / ID: 4hex
TitleA novel conformation of calmodulin
ComponentsCalmodulin
KeywordsCALCIUM BINDING PROTEIN / Calmodulin / Novel conformation / trans / EF-hand motifs / Calcium signalling / Calcium binding / Neuromodulin / Neurogranin
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol ...CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calcineurin activates NFAT / eNOS activation / Ion transport by P-type ATPases / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / Smooth Muscle Contraction / Ca2+ pathway / negative regulation of calcium ion transmembrane transporter activity / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Platelet degranulation / : / Stimuli-sensing channels / establishment of protein localization to mitochondrial membrane / Ion homeostasis / type 3 metabotropic glutamate receptor binding / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / potassium ion transmembrane transport / voltage-gated potassium channel complex / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / sperm midpiece / calcium channel complex / activation of adenylate cyclase activity / response to amphetamine / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / calcium-mediated signaling / positive regulation of nitric-oxide synthase activity / mitochondrial membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / synaptic vesicle membrane / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding
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-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsKumar, V. / Chichili, V.P.R. / Sivaraman, J.
CitationJournal: Plos One / Year: 2013
Title: A novel trans conformation of ligand-free calmodulin
Authors: Kumar, V. / Chichili, V.P.R. / Tang, X. / Sivaraman, J.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17812
Polymers35,6252
Non-polymers55310
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-281 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.827, 116.397, 38.797
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 7 - 143 / Label seq-ID: 14 - 150

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Calmodulin / / CaM


Mass: 17812.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cam / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62204, UniProt: P0DP26*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#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 / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris-HCl, 8-10%(v/v) PEG 6K, 5-10mM ZnCl2, 10%(v/v) glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.526
11L, -K, H20.474
ReflectionResolution: 2.001→50 Å / Num. obs: 22800 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.381 / Num. unique all: 2341 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029refinement
RefinementMethod to determine structure: SAD / Resolution: 2.001→28.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.549 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1191 5.2 %RANDOM
Rwork0.2098 21561 --
obs0.2112 21561 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.48 Å2 / Biso mean: 47.251 Å2 / Biso min: 25 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å22.89 Å2
2---6.16 Å20 Å2
3---4.92 Å2
Refinement stepCycle: LAST / Resolution: 2.001→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 10 78 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192227
X-RAY DIFFRACTIONr_bond_other_d0.0050.022022
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9642992
X-RAY DIFFRACTIONr_angle_other_deg1.27434686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98526.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5311512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022595
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02469
Refine LS restraints NCS

Ens-ID: 1 / Number: 6834 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 69 -
Rwork0.324 1401 -
all-1470 -
obs--84.82 %
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)
10.1786-0.7447-0.093.32640.13750.4522-0.01040.0423-0.04640.1552-0.05580.1585-0.0481-0.12810.06620.09630.0152-0.02590.1589-0.00470.0252-17.23528.482713.5912
20.2196-0.2596-0.02052.38630.64950.26360.04560.10350.0136-0.1003-0.025-0.1589-0.00970.0044-0.02060.0859-0.0064-0.01050.1595-0.00720.0235-5.7991-7.83263.3641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 144
2X-RAY DIFFRACTION1A201 - 204
3X-RAY DIFFRACTION2B7 - 146
4X-RAY DIFFRACTION2B201 - 204

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