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- PDB-4l11: Structure of the C-linker/CNBHD of agERG channels -

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Basic information

Entry
Database: PDB / ID: 4l11
TitleStructure of the C-linker/CNBHD of agERG channels
ComponentsAGAP007709-PA
KeywordsMETAL TRANSPORT / CNBHD / CNBD / KCNH / cyclic nucleotide binding domain / ion transport
Function / homology
Function and homology information


voltage-gated potassium channel activity / monoatomic ion channel complex / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, ERG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS 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 ...Potassium channel, voltage-dependent, ERG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS 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 domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBrelidze, T.I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of the C-terminal region of an ERG channel and functional implications.
Authors: Brelidze, T.I. / Gianulis, E.C. / Dimaio, F. / Trudeau, M.C. / Zagotta, W.N.
History
DepositionJun 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGAP007709-PA


Theoretical massNumber of molelcules
Total (without water)23,2991
Polymers23,2991
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 51.400, 162.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein AGAP007709-PA


Mass: 23298.578 Da / Num. of mol.: 1 / Fragment: C-linker/CNBHD (unp residues 535-734)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: AGAP007709, AgaP_AGAP007709, ERG / Plasmid: pMALc2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q7QJX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 9 mM Urea, 18.2% (w/v) PEG 3350, 7.3 % (v/v) Tacsimate , pH 7.0, 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: Oct 22, 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: 2.55→40.51 Å / Num. obs: 8662 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 3.3 / % possible all: 100

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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: PDB ENTRY 3UKN

3ukn


Resolution: 2.55→34.351 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 405 4.76 %
Rwork0.2193 --
obs0.2209 8511 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.287 Å2 / ksol: 0.345 e/Å3
Refinement stepCycle: LAST / Resolution: 2.55→34.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 0 18 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091553
X-RAY DIFFRACTIONf_angle_d1.3332119
X-RAY DIFFRACTIONf_dihedral_angle_d16.116538
X-RAY DIFFRACTIONf_chiral_restr0.089244
X-RAY DIFFRACTIONf_plane_restr0.004276
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)
10.32550.154-0.3180.1476-0.1650.1447-0.26820.20040.58960.1963-0.1268-0.0215-0.9377-0.26140.00110.8471-0.06220.00720.34890.04760.66124.3657-31.942219.3274
20.6871-0.0516-0.55820.40540.04020.4040.88742.6945-0.7391-1.073-1.61190.14280.038-2.5056-0.01380.9616-0.28910.02640.9108-0.26130.846414.2099-27.609216.0195
30.2411-0.1883-0.26570.11020.17640.2305-0.2091-0.3353-0.6903-1.78522.0645-1.78760.75840.978-0.0021.2676-0.07380.0020.84430.09151.415823.4353-25.758219.0485
40.38440.36-0.22050.2912-0.1350.210.331-0.1116-0.83931.3997-0.5001-0.36751.1924-0.9035-0.00111.252-0.0852-0.0480.53790.17710.832114.7909-28.412727.5113
50.95510.10920.23130.03380.07210.21560.94691.67680.87450.21450.94962.96691.25350.3313-0.01761.49810.52580.05140.5090.12381.17241.646-27.739124.7003
60.49110.35890.20110.6690.12220.077-0.38910.85120.546-0.4239-0.66170.71942.5789-1.1516-0.01131.05820.06340.33281.0001-0.02181.78937.5249-20.694718.6755
70.1385-0.009-0.1084-0.0392-0.00250.09440.12810.6673-0.2214-0.25660.84220.07180.0107-1.1531-0.00061.2332-0.24360.27210.74060.26211.116116.2297-17.801127.435
8-0.0060.0075-0.01650.1130.12760.1112-0.13390.3471-0.6354-2.1038-0.5811.4592-1.4988-0.2214-0.00470.74410.0726-0.15140.29140.00970.836423.6635-15.804519.7926
90.73960.33230.54070.66860.23310.40320.1527-0.0705-0.9801-0.6516-0.1368-0.2860.50740.3385-0.0020.67570.1065-0.04120.3601-0.0770.791932.3232-10.953213.4844
100.1291-0.23820.30341.6317-0.00470.5160.5104-0.33040.20630.677-0.14960.07710.8887-0.04050.00110.636-0.04030.05050.29180.05960.377526.685-7.965519.0444
110.2149-0.06070.18970.0145-0.06720.1091-0.2479-0.138-1.28642.297-0.7460.5356-0.0177-0.7908-0.00120.8016-0.0639-0.08251.33770.10290.66149.0038-10.84844.5982
120.77861.07071.26641.66010.05121.58760.0592-0.2776-0.21520.3176-0.17260.46360.4372-0.50080.00040.47720.019-0.02830.4796-0.02870.442416.3735-4.07235.6823
131.68421.319-0.19451.37340.71851.05050.0754-0.03680.25830.1640.16630.16790.11590.309200.5504-0.05690.00250.5953-0.12430.407118.5549-5.9576-2.3275
140.3179-0.0712-0.29740.0969-0.040.2555-0.12490.05610.12540.02630.2299-0.2337-0.28740.75740.00030.59060.0410.04050.47830.08850.591425.8647.19218.8986
150.20240.3555-0.18880.2845-0.20450.1006-0.97840.56360.2496-1.00040.62560.1641-1.2879-0.35110.00020.7250.0307-0.11220.55550.00330.559514.82923.36413.1252
160.4281-0.2207-0.13950.37610.39240.31530.7883-0.9782-0.15960.8741-0.55131.02782.037-2.01720.0020.9169-0.2333-0.09710.70030.0180.709614.7114-15.39194.6209
170.72680.16290.93050.449-0.11631.6955-0.18850.4257-0.060.38880.38660.4305-0.27960.052-00.51560.00080.05250.33390.01630.339625.6231.338118.3376
180.5232-0.18830.05940.07930.24510.5563-0.2007-0.26490.00470.5286-0.2034-0.2531-0.3475-0.3787-0.00130.46090.048-0.00470.41470.02890.36535.57591.790511.8148
190.4632-0.19710.38282.4627-0.87660.5331-0.77190.87580.666-0.13311.6171.1390.07991.85190.03740.532-0.0613-0.06040.7519-0.09720.298325.4283-1.56870.4251
200.3472-0.0439-0.2971-0.0110.03510.22190.4460.81410.30292.4420.5144-0.1494-0.3655-1.4103-0.00120.72320.13230.07140.5510.17670.64718.90487.94950.1874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 537:544)
2X-RAY DIFFRACTION2(chain A and resid 545:551)
3X-RAY DIFFRACTION3(chain A and resid 552:560)
4X-RAY DIFFRACTION4(chain A and resid 561:571)
5X-RAY DIFFRACTION5(chain A and resid 572:575)
6X-RAY DIFFRACTION6(chain A and resid 576:584)
7X-RAY DIFFRACTION7(chain A and resid 585:594)
8X-RAY DIFFRACTION8(chain A and resid 595:600)
9X-RAY DIFFRACTION9(chain A and resid 601:611)
10X-RAY DIFFRACTION10(chain A and resid 612:630)
11X-RAY DIFFRACTION11(chain A and resid 631:636)
12X-RAY DIFFRACTION12(chain A and resid 637:655)
13X-RAY DIFFRACTION13(chain A and resid 656:673)
14X-RAY DIFFRACTION14(chain A and resid 674:680)
15X-RAY DIFFRACTION15(chain A and resid 681:690)
16X-RAY DIFFRACTION16(chain A and resid 691:697)
17X-RAY DIFFRACTION17(chain A and resid 698:713)
18X-RAY DIFFRACTION18(chain A and resid 714:723)
19X-RAY DIFFRACTION19(chain A and resid 724:728)
20X-RAY DIFFRACTION20(chain A and resid 729:734)

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