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- PDB-5hit: Crystal Structure Analysis of Ca2+-calmodulin and a C-terminal EA... -

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Basic information

Entry
Database: PDB / ID: 5hit
TitleCrystal Structure Analysis of Ca2+-calmodulin and a C-terminal EAG1 channel fragment
Components
  • Calmodulin
  • Potassium voltage-gated channel subfamily H member 1
KeywordsSIGNALING PROTEIN / calmodulin / potassium channel
Function / homology
Function and homology information


Voltage gated Potassium channels / CH domain binding / : / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / nuclear inner membrane ...Voltage gated Potassium channels / CH domain binding / : / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / myosin binding / startle response / voltage-gated potassium channel activity / plasma membrane => GO:0005886 / phosphatidylinositol-mediated signaling / axolemma / enzyme regulator activity / monoatomic ion transmembrane transport / potassium ion transmembrane transport / voltage-gated potassium channel complex / 14-3-3 protein binding / cellular response to calcium ion / regulation of membrane potential / postsynaptic density membrane / disordered domain specific binding / presynaptic membrane / regulation of cell population proliferation / early endosome membrane / perikaryon / transmembrane transporter binding / calmodulin binding / axon / intracellular membrane-bounded organelle / neuronal cell body / synapse / calcium ion binding / dendrite / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein-containing complex / identical protein binding / plasma membrane
Similarity search - Function
Potassium voltage-gated channel subfamily H member 1 / Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...Potassium voltage-gated channel subfamily H member 1 / Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PAS repeat profile. / RmlC-like jelly roll fold / PAS domain / PAS domain superfamily / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin / Potassium voltage-gated channel subfamily H member 1 / Potassium voltage-gated channel subfamily H member 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsMarques-Carvalho, M.J. / Morais-Cabral, J.H.
CitationJournal: Structure / Year: 2016
Title: Molecular Insights into the Mechanism of Calmodulin Inhibition of the EAG1 Potassium Channel.
Authors: Marques-Carvalho, M.J. / Oppermann, J. / Munoz, E. / Fernandes, A.S. / Gabant, G. / Cadene, M. / Heinemann, S.H. / Schonherr, R. / Morais-Cabral, J.H.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Oct 19, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7024
Polymers18,6222
Non-polymers802
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-22 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.624, 121.137, 73.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Calmodulin / CaM


Mass: 16592.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM, CAM, RCJMB04_24e7 / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62149
#2: Protein/peptide Potassium voltage-gated channel subfamily H member 1


Mass: 2029.433 Da / Num. of mol.: 1 / Fragment: UNP residues 727-743
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnh1 / Plasmid: pRSF Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3USQ9, UniProt: Q60603*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: di-ammonium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2014 / Details: microfocus beam
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.85→46.83 Å / Num. obs: 5817 / % possible obs: 99.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.04 / Net I/σ(I): 15.3 / Num. measured all: 23869
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.85-34.20.6132.735408360.7950.33499.4
9.01-46.833.50.01944.67412090.9990.01298.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CFD, 3OXQ

1cfd

3oxq


Resolution: 2.85→46.83 Å / FOM work R set: 0.7844 / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1017 9.49 %
Rwork0.2047 9694 -
obs0.2107 5814 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.85 Å2 / Biso mean: 52.91 Å2 / Biso min: 13.09 Å2
Refinement stepCycle: final / Resolution: 2.85→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 2 10 1257
Biso mean--39.74 42.65 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041276
X-RAY DIFFRACTIONf_angle_d0.4431749
X-RAY DIFFRACTIONf_chiral_restr0.032192
X-RAY DIFFRACTIONf_plane_restr0.002229
X-RAY DIFFRACTIONf_dihedral_angle_d10.12471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-3.00030.38831240.31131419154399
3.0003-3.18820.29471490.27891375152499
3.1882-3.43430.33141560.25011367152399
3.4343-3.77980.27231650.19911373153899
3.7798-4.32640.24431460.16181393153999
4.3264-5.44950.25411300.18341396152698
5.4495-46.83970.2381470.19381371151898
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)
10.0123-0.0007-0.00070.006-0.0005-0.0007-0.0025-0.0304-0.0385-0.0014-0.0274-0.01990.01490.02250-0.14910.38220.05430.1135-0.050.125363.179627.2328-25.0988
2-0.0083-0.01340.0132-0.0085-0.0055-0.00530.0286-0.0320.01430.0272-0.0170.0158-0.02880.037200.14640.2857-0.15610.09430.03450.214967.588723.4322-9
30.00470.0003-0.00060.0067-0.0040.00290.009-0.0176-0.0511-0.01810.0613-0.03110.0380.0291-00.27420.047-0.0040.136-0.01650.231678.622210.46665.075
40.00210.00010-0.0002-0.00020.00330.0041-0.00630.0030.00710.00020.01020.0044-0.0071-00.34250.0536-0.01420.4777-0.08550.344364.295321.13967.7757
50.00060.00070.00080.0003-0.0006-0.0005-0.01280.00250.00130.0033-0.00690.0014-0.01080.0013-00.3485-0.1433-0.0360.34930.01160.407965.539212.13392.9435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 64 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 147 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 727 through 735 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 736 through 743 )B0

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