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- PDB-3ukv: Structure of the C-linker/CNBHD of zELK channels in P 1 21 1 spac... -

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Basic information

Entry
Database: PDB / ID: 3ukv
TitleStructure of the C-linker/CNBHD of zELK channels in P 1 21 1 space group, crystallized in the presence of cAMP
ComponentsNovel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / KCNH / ELK / ERG / EAG / CNBD / CNBHD / cyclic nucleotide / cyclic nucleotide-binding domain / ion transport
Function / homology
Function and homology information


CNBH domain intrinsic ligand binding / potassium ion transmembrane transporter activity / monoatomic ion channel complex / voltage-gated potassium channel activity / potassium channel activity / potassium ion import across plasma membrane / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #260 / Potassium channel, voltage-dependent, ELK / 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) / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Cyclic nucleotide-monophosphate binding domain ...Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #260 / Potassium channel, voltage-dependent, ELK / 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) / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / PAS repeat profile. / RmlC-like jelly roll fold / PAS domain / PAS domain superfamily / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Potassium voltage-gated channel, subfamily H (eag-related), member 3
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBrelidze, T.I.
CitationJournal: Nature / Year: 2012
Title: Structure of the carboxy-terminal region of a KCNH channel.
Authors: Brelidze, T.I. / Carlson, A.E. / Sankaran, B. / Zagotta, W.N.
History
DepositionNov 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Jun 6, 2012Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
A: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
C: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
D: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family


Theoretical massNumber of molelcules
Total (without water)96,2874
Polymers96,2874
Non-polymers00
Water81145
1
B: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
A: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family


Theoretical massNumber of molelcules
Total (without water)48,1442
Polymers48,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-22 kcal/mol
Surface area18320 Å2
MethodPISA
2
C: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
D: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family


Theoretical massNumber of molelcules
Total (without water)48,1442
Polymers48,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-14 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.330, 106.420, 77.520
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family


Mass: 24071.785 Da / Num. of mol.: 4 / Fragment: unp residues 543-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: CH211-11O22.2-001, ELK, KCNH3 / Plasmid: pMALc2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A8WHX9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5 mM cAMP, 180 mM ammonium acetate, 22.5% (w/v) PEG 3350, 90 mM TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.76 Å / Num. all: 24491 / Num. obs: 24491 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3537 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
BOSdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF THE CORRESPONDING SELENOMETHIONINE DERIVATIVE CRYSTAL

Resolution: 2.7→48.759 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 31.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 1167 4.98 %
Rwork0.2152 --
obs0.2183 23411 95.4 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.033 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6823 Å20 Å2-5.6602 Å2
2--11.5006 Å20 Å2
3----7.8183 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 0 45 5306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095343
X-RAY DIFFRACTIONf_angle_d1.2537256
X-RAY DIFFRACTIONf_dihedral_angle_d14.2071860
X-RAY DIFFRACTIONf_chiral_restr0.073880
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.82290.39021270.30552444X-RAY DIFFRACTION85
2.8229-2.97170.37941340.29452624X-RAY DIFFRACTION90
2.9717-3.15780.41261450.26362724X-RAY DIFFRACTION95
3.1578-3.40160.31481510.23462834X-RAY DIFFRACTION97
3.4016-3.74380.28381490.21272864X-RAY DIFFRACTION98
3.7438-4.28530.26491510.19032899X-RAY DIFFRACTION99
4.2853-5.39790.21951540.16952894X-RAY DIFFRACTION100
5.3979-48.76680.2481560.22432961X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1810.1680.2422-0.1295-0.019-0.0829-0.10220.03720.2522-0.04110.06190.1279-0.08640.01330.00420.3419-0.01350.06650.2368-0.00850.3602-10.117313.2462-3.8654
22.72861.17170.60252.6980.68251.1139-0.60270.10350.2725-0.1780.33670.62620.01910.20020.1540.3004-0.0423-0.06360.26960.08850.4235-12.223918.3582-18.0505
35.03972.0444-0.78492.4840.32450.7265-0.33050.5034-0.634-0.03940.5673-0.2416-0.0094-0.184-0.00790.3592-0.03610.04980.3783-0.02420.3167-19.93574.0329-18.5789
42.06010.0379-0.03090.3096-0.27740.2646-0.0769-0.0530.00060.0475-0.0304-0.0463-0.04080.01780.08560.3727-0.02860.01680.25450.00770.4021.33118.00512.0641
51.5021-0.1464-0.16020.60770.08032.465-0.0987-0.0047-0.13910.11970.06220.17210.4760.0243-0.00510.3709-0.028-0.00540.22760.03750.3313.3571-5.66439.0137
62.33310.339-0.78740.91151.20052.25290.13590.2951-0.5168-0.1856-0.08470.09550.5005-0.02170.0340.4920.00910.00840.2427-0.03520.385911.2184-7.4498-5.5629
73.3775-0.32210.63510.31721.04973.56210.1095-0.8689-0.2762-0.0549-0.0019-0.07130.5729-0.0024-0.20.2489-0.0327-0.02460.34240.03370.356418.184525.280930.0292
83.41571.8023-0.14740.9261-0.05882.42020.0750.00270.2762-0.07280.00690.214-0.1377-0.1774-0.07490.205-0.00270.10420.14850.00110.23445.776422.083421.9229
92.0797-0.46220.79262.33960.31852.2418-0.38550.12740.7721-0.30310.24670.6012-0.2333-0.03430.14040.2497-0.01520.03710.16530.01690.328712.702633.725912.9916
102.12870.2811-0.1910.30060.78962.38770.4104-0.94570.0938-0.0189-0.1319-0.09150.05630.5658-0.20650.5532-0.1479-0.03060.5966-0.00910.422825.278429.796139.1551
113.6022.19350.39351.68620.27682.8957-0.7214-0.68540.1471-0.0824-0.3816-0.0992-0.58680.0980.45750.39920.0082-0.08230.2826-0.1870.355729.300943.119148.1559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 550:640 )A550 - 640
2X-RAY DIFFRACTION2( CHAIN A AND RESID 641:712 )A641 - 712
3X-RAY DIFFRACTION3( CHAIN A AND RESID 713:744 )A713 - 744
4X-RAY DIFFRACTION4( CHAIN B AND RESID 548:640 )B548 - 640
5X-RAY DIFFRACTION5( CHAIN B AND RESID 641:712 )B641 - 712
6X-RAY DIFFRACTION6( CHAIN B AND RESID 713:743 )B713 - 743
7X-RAY DIFFRACTION7( CHAIN C AND RESID 552:640 )C552 - 640
8X-RAY DIFFRACTION8( CHAIN C AND RESID 641:712 )C641 - 712
9X-RAY DIFFRACTION9( CHAIN C AND RESID 713:744 )C713 - 744
10X-RAY DIFFRACTION10( CHAIN D AND RESID 549:640 )D549 - 640
11X-RAY DIFFRACTION11( CHAIN D AND RESID 641:712 )D641 - 712

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