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- PDB-3ukn: Structure of the C-linker/CNBHD of zELK channels in C 2 2 21 spac... -

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Basic information

Entry
Database: PDB / ID: 3ukn
TitleStructure of the C-linker/CNBHD of zELK channels in C 2 2 21 space group
ComponentsNovel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / KCNH / ELK / ERG / EAG / CNBD / CNBHD / C-linker / Ion Channel / 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
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) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...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) / 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 / Mainly Beta
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: 2.2 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
A: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
B: 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


Theoretical massNumber of molelcules
Total (without water)72,2153
Polymers72,2153
Non-polymers00
Water5,945330
1
A: Novel protein similar to vertebrate potassium voltage-gated channel, subfamily H (Eag-related) family
B: 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 area2480 Å2
ΔGint-21 kcal/mol
Surface area18880 Å2
MethodPISA
2
C: 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


Theoretical massNumber of molelcules
Total (without water)48,1442
Polymers48,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2300 Å2
ΔGint-25 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.980, 95.480, 241.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 3 / 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.: 330 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.8 M non-detergent sulfobetaine (NDSB)-211, 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: 2.2→49.56 Å / Num. all: 33782 / Num. obs: 33782 / % possible obs: 97.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4271 / % possible all: 85.4

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of the corresponding selenomethionine derivative crystal

Resolution: 2.2→49.558 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 1676 4.98 %
Rwork0.2125 --
obs0.2146 33676 97.47 %
all-33675 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.132 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4107 Å2-0 Å20 Å2
2---1.0799 Å2-0 Å2
3---5.4907 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 0 330 4726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084462
X-RAY DIFFRACTIONf_angle_d1.0926045
X-RAY DIFFRACTIONf_dihedral_angle_d12.5251601
X-RAY DIFFRACTIONf_chiral_restr0.073729
X-RAY DIFFRACTIONf_plane_restr0.004760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.45181380.45352594X-RAY DIFFRACTION81
2.2786-2.36990.34391560.29113075X-RAY DIFFRACTION95
2.3699-2.47770.31011750.26063226X-RAY DIFFRACTION100
2.4777-2.60830.33521670.24313250X-RAY DIFFRACTION100
2.6083-2.77170.30961710.23333264X-RAY DIFFRACTION100
2.7717-2.98570.27051620.21433259X-RAY DIFFRACTION100
2.9857-3.28610.22451840.19453274X-RAY DIFFRACTION100
3.2861-3.76150.22071720.19723279X-RAY DIFFRACTION100
3.7615-4.73850.20881700.15993328X-RAY DIFFRACTION100
4.7385-49.57080.23411810.20383451X-RAY DIFFRACTION100
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)
11.37111.32610.44041.66031.16860.64290.0933-0.16420.12680.067-0.13750.19420.0711-0.0560.00170.1209-0.00310.02080.06150.02960.07354.344932.867118.3722
20.065-0.37180.32751.1306-0.18440.65330.03710.0457-0.1054-0.1803-0.09770.03410.06670.10720.0510.085-0.00670.02330.06330.06050.1865-3.12534.67045.5205
30.8482-1.1987-0.20770.8597-0.26010.00740.16470.046-0.213-0.2017-0.0732-0.0129-0.03480.0263-0.08260.17750.05210.00740.1012-0.01630.22455.053521.16912.4858
42.48080.9340.52371.10880.68530.01060.2666-0.36240.32070.2583-0.21740.0579-0.0555-0.0804-0.03980.13780.00410.01710.1835-0.0240.092515.474739.317523.5068
52.08540.54620.05211.883-0.68020.37460.156-0.474-0.0558-0.0655-0.2841-0.08060.11690.15570.07910.1685-0.03510.00760.28250.05230.135928.865834.049428.023
61.52340.7528-0.44022.7006-0.7311.1699-0.41940.0260.0226-0.41140.0708-0.19320.08430.04640.30120.2060.02140.04090.14630.010.12832.984440.244713.8231
70.1753-0.61670.17640.5439-0.35012.2159-0.44160.05690.1466-0.02040.3444-0.20770.1893-0.3675-0.03160.06520.00250.10.52020.01530.0881-2.903338.418653.748
80.5703-0.1867-1.19472.23560.10464.2101-0.0910.52240.00890.03150.0610.30790.0291-2.161-0.01550.10560.08920.00741.09400.1497-15.871843.001148.3555
91.9686-1.00542.66161.3173-1.30626.2744-0.42-0.0053-0.1787-0.4513-0.2629-0.1968-1.2089-0.28020.26730.52550.0393-0.09620.45340.26910.6444-5.412454.011842.588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 549:640 )A549 - 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 713:745 )B713 - 745
7X-RAY DIFFRACTION7( CHAIN C AND RESID 549:640 )C549 - 640
8X-RAY DIFFRACTION8( CHAIN C AND RESID 641:712 )C641 - 712
9X-RAY DIFFRACTION9( CHAIN C AND RESID 713:743 )C713 - 743

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