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- PDB-4hoi: Crystal structure of PAS domain from the mouse EAG1 potassium channel -

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Basic information

Entry
Database: PDB / ID: 4hoi
TitleCrystal structure of PAS domain from the mouse EAG1 potassium channel
ComponentsPotassium voltage-gated channel subfamily H member 1
KeywordsTRANSPORT PROTEIN / Potassium channel domain
Function / homology
Function and homology information


Voltage gated Potassium channels / 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 / parallel fiber to Purkinje cell synapse / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / startle response ...Voltage gated Potassium channels / 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 / parallel fiber to Purkinje cell synapse / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / startle response / axolemma / potassium ion transmembrane transport / voltage-gated potassium channel complex / monoatomic ion transmembrane transport / 14-3-3 protein binding / cellular response to calcium ion / regulation of membrane potential / postsynaptic density membrane / presynaptic membrane / regulation of cell population proliferation / early endosome membrane / perikaryon / transmembrane transporter binding / calmodulin binding / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / 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 / Beta-Lactamase / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily H member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsAdaixo, R. / Morais-Cabral, J.H.
Citation
Journal: Plos One / Year: 2013
Title: Structural properties of PAS domains from the KCNH potassium channels
Authors: Adaixo, R. / Harley, C.A. / Castro-Rodrigues, A.F. / Morais-Cabral, J.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels
Authors: Adaixo, R. / Morais-Cabral, J.H.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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_initial_refinement_model / 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 / _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: Potassium voltage-gated channel subfamily H member 1
B: Potassium voltage-gated channel subfamily H member 1
C: Potassium voltage-gated channel subfamily H member 1
D: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,78510
Polymers53,2094
Non-polymers5766
Water7,116395
1
A: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3982
Polymers13,3021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4943
Polymers13,3021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3982
Polymers13,3021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4943
Polymers13,3021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Potassium voltage-gated channel subfamily H member 1
hetero molecules

D: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8935
Polymers26,6042
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area11440 Å2
MethodPISA
6
B: Potassium voltage-gated channel subfamily H member 1
C: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8935
Polymers26,6042
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.276, 91.276, 172.521
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is most likely a monomer. There are 4 biological units in the asymmetric unit

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Components

#1: Protein
Potassium voltage-gated channel subfamily H member 1 / Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel ...Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel subunit Kv10.1


Mass: 13302.239 Da / Num. of mol.: 4 / Fragment: PAS domain of KCNH1 channel, UNP residues 28-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eag, Kcnh1 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q60603
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3M ammonium sulfate, 0.25M lithium sulfate, 0.1M Tris-HCl, pH 8.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→79.06 Å / Num. all: 71849 / Num. obs: 71849 / % possible obs: 100 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 1.3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.85-1.955.50.5631.30.5631100
1.95-2.075.50.3432.20.3431100
2.07-2.215.50.2122.30.2121100
2.21-2.395.50.1534.70.1531100
2.39-2.629.30.1564.50.1561100
2.62-2.9311.10.116.40.111100
2.93-3.38110.077.70.071100
3.38-4.1410.90.0512.60.051100
4.14-5.8510.70.04213.60.0421100
5.85-43.1539.60.03913.70.039199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BYW

1byw


Resolution: 1.85→40.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.15 / SU R Cruickshank DPI: 0.0996 / σ(F): 1.36 / Phase error: 18.01 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1924 3629 5.06 %
Rwork0.1664 --
obs0.1677 71734 99.97 %
all-71743 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8497 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å2-0 Å2
2--0.34 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 30 395 4100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113924
X-RAY DIFFRACTIONf_angle_d1.2145335
X-RAY DIFFRACTIONf_dihedral_angle_d13.0361458
X-RAY DIFFRACTIONf_chiral_restr0.081576
X-RAY DIFFRACTIONf_plane_restr0.005672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.85-1.87430.23871430.24282591
1.8743-1.90.23661390.2192613
1.9-1.92720.2815980.2082587
1.9272-1.95590.22051170.19852597
1.9559-1.98650.23681390.20382626
1.9865-2.01910.21351330.1952590
2.0191-2.05390.20561460.17632568
2.0539-2.09120.20051280.17452567
2.0912-2.13140.19971460.16762593
2.1314-2.17490.21811430.16612607
2.1749-2.22220.2081500.16552599
2.2222-2.27390.22271190.1622608
2.2739-2.33080.18981510.15892576
2.3308-2.39380.18191610.15682613
2.3938-2.46420.19171290.16292621
2.4642-2.54370.22721380.17212596
2.5437-2.63460.19351370.17622593
2.6346-2.74010.21341600.17652586
2.7401-2.86480.20841490.18062630
2.8648-3.01580.20051410.18212608
3.0158-3.20470.20711250.17772654
3.2047-3.4520.19741350.16662662
3.452-3.79910.17581630.14872628
3.7991-4.34830.1631620.13212650
4.3483-5.47620.14651430.12372702
5.4762-40.34970.19331340.20152840
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)
14.92381.2639-2.38115.1257-1.37754.6739-0.09190.1640.2918-0.01990.12850.1207-0.0137-0.0895-0.03270.19360.1183-0.02410.2005-0.04070.239910.496656.923547.4411
25.0537-3.0978-2.3123.01112.26712.0825-0.2271-0.4507-0.26880.54160.3325-0.29870.67040.6061-0.09780.35990.1781-0.04610.3229-0.03830.246416.406547.852250.266
33.6227-2.673-1.20883.51260.90312.19690.41520.14210.3671-0.8973-0.132-0.3821-0.9001-0.1682-0.15380.48540.18440.03230.23690.01670.277415.277455.686536.1101
43.1371-2.2968-0.96464.3060.83341.63810.07090.0914-0.1884-0.2325-0.07220.2081-0.4137-0.3043-0.01740.42810.2292-0.06390.3048-0.05760.245312.079150.923337.2675
51.1302-2.0145-1.50024.00692.75081.90540.33610.3023-0.1402-0.1865-0.52880.17190.013-0.33490.05990.22660.3629-0.06510.1667-0.14640.3026.984551.486940.6348
62.8539-1.5309-0.82745.70913.54423.8715-0.01370.1864-0.15640.1305-0.16360.2860.1088-0.11120.1530.19550.0853-0.02970.2282-0.05740.21815.161154.911644.4888
76.28160.06594.59234.35440.54555.994-0.00380.43460.0622-0.2664-0.13260.22010.03350.21020.08520.28820.09820.02990.2374-0.06890.239222.993721.223217.3985
85.8258-2.7365-1.66815.32013.31934.3553-0.2668-0.3353-0.23120.5823-0.29540.90020.3424-0.60790.53120.31560.0310.10770.2454-0.08040.33316.637319.627826.6603
93.5617-2.4065-1.38825.62251.38481.92110.03970.35780.1094-0.9776-0.23850.2764-0.5623-0.69990.17230.47360.2114-0.10840.3037-0.07070.241417.60732.089516.4887
103.9797-1.0991-1.64163.92732.66345.2421-0.01530.25760.1457-1.0158-0.1553-0.1422-0.5092-0.23490.16070.47720.120.03310.20820.00080.245524.690232.300117.3888
110.7776-0.591-0.80313.77561.35832.8869-0.14050.0149-0.00440.0155-0.07510.125-0.0958-0.33890.22670.25990.09070.00380.2071-0.05440.235521.972429.154623.7651
122.001-4.5539-5.03174.80820.23023.73120.30990.9743-0.34-1.5266-0.6767-0.36530.2095-0.27980.23580.5390.08650.13540.2464-0.03970.300332.846113.48324.9215
131.4203-2.1301-1.79965.73895.09126.7341-0.1564-0.10340.1315-0.0176-0.0414-0.1316-0.1125-0.0650.16660.29940.0749-0.00010.1541-0.02060.231326.190128.179423.3167
143.37060.72931.83912.44931.1941.82080.0599-0.113-0.05040.2019-0.0827-0.0071-0.67140.06460.06040.3095-0.03490.03520.1301-0.02050.192330.73899.046220.8696
154.3553-0.1741-1.00995.53861.89878.5689-0.01510.1651-0.14720.0057-0.21381.14920.1596-0.84110.26320.23260.00070.02050.2211-0.08950.395721.38453.081714.8721
168.7311-3.2557-0.3242.71481.68793.34230.0493-0.3387-0.64690.48570.09210.36950.6616-0.0539-0.08960.3881-0.02820.04010.1150.01960.280930.4846-3.520720.7263
173.2629-3.08910.77983.41780.35672.60390.0438-0.5707-0.62851.2320.193-1.36920.47710.4443-0.2070.41870.0908-0.1150.21620.0010.478341.8048-1.10621.7314
185.83115.20460.53448.9921-1.10792.3363-0.0577-0.0213-0.1823-0.02620.043-1.16730.1120.19870.02970.28290.01710.02280.1881-0.06180.370639.12560.83215.4136
190.85770.49850.02033.35261.50862.7415-0.07930.0129-0.02930.01560.1102-0.01130.00820.0547-0.0610.27810.01510.04610.1355-0.05030.262333.51874.875414.8458
201.83821.40070.79776.30182.5873.9887-0.06530.2386-0.2326-0.4552-0.0215-0.07890.34890.03110.02760.36470.02240.08480.1528-0.04180.25933.70162.542110.3669
218.728-4.6389-0.76856.56741.31752.7903-0.0945-0.11260.2256-0.31250.1852-0.3860.22570.2633-0.04060.3380.0616-0.0320.1479-0.00960.220142.273125.407954.8277
223.7276-2.94940.96736.1296-1.69327.42880.06540.0087-0.2716-0.431-0.09680.55350.4034-0.49350.05910.34030.0115-0.10410.1059-0.02730.263530.551123.528152.085
233.7025-0.75230.71343.4232-0.36631.8920.25040.005-0.2849-0.4375-0.00790.1405-0.4269-0.1333-0.17960.4950.0548-0.10280.1404-0.03230.244732.329518.479247.9613
244.98576.2606-4.74067.8559-5.95034.50480.0090.1488-0.4042-0.67630.0114-0.27940.08420.0870.10040.41180.0487-0.02010.1764-0.03170.240440.874321.831649.1955
256.78431.5821-1.30933.5471-4.70016.3253-0.15430.58650.0246-0.94420.19610.2578-0.20040.0969-0.02880.65760.0730.03170.27560.01760.192338.713730.09338.199
263.9567-0.36473.77982.9493-1.39773.9822-0.14621.05840.1641-1.0443-0.0112-0.6201-0.23991.06650.16790.4593-0.02330.07970.35530.01820.276447.081935.298345.4673
274.49251.16233.67092.72680.99513.0214-0.26150.36690.3577-0.7010.02280.1501-0.38570.40840.27350.4095-0.005-0.0510.20270.03080.243540.464536.378148.2394
285.5443-1.28263.32944.2426-6.55822.00230.1440.1823-0.07110.34450.011-0.74280.4339-0.20160.06220.56430.079-0.13070.2183-0.09550.313829.089424.878137.5595
293.7698-1.58333.53831.2408-1.43275.6932-0.3881-0.02660.2296-0.31750.04610.0756-0.5695-0.16380.24680.43440.0086-0.13380.1338-0.010.247736.264834.968550.2498
303.43313.5767-4.10843.7273-4.27964.922-0.293-1.0255-0.03070.81650.2651-1.1822-0.85291.72710.15720.34950.0294-0.12920.40230.00870.317249.659531.538469.1171
313.8409-1.36031.16984.7501-1.4283.3781-0.4043-0.18480.5711-0.20450.1990.3353-0.445-0.51360.12040.34170.0859-0.10040.1966-0.02480.273735.199734.484453.7677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 25:41)
2X-RAY DIFFRACTION2chain A and (resseq 42:60)
3X-RAY DIFFRACTION3chain A and (resseq 61:88)
4X-RAY DIFFRACTION4chain A and (resseq 89:105)
5X-RAY DIFFRACTION5chain A and (resseq 106:117)
6X-RAY DIFFRACTION6chain A and (resseq 118:137)
7X-RAY DIFFRACTION7chain B and (resseq 24:41)
8X-RAY DIFFRACTION8chain B and (resseq 42:60)
9X-RAY DIFFRACTION9chain B and (resseq 61:88)
10X-RAY DIFFRACTION10chain B and (resseq 89:100)
11X-RAY DIFFRACTION11chain B and (resseq 101:117)
12X-RAY DIFFRACTION12chain B and (resseq 118:122)
13X-RAY DIFFRACTION13chain B and (resseq 123:137)
14X-RAY DIFFRACTION14chain C and (resseq 28:41)
15X-RAY DIFFRACTION15chain C and (resseq 42:60)
16X-RAY DIFFRACTION16chain C and (resseq 61:76)
17X-RAY DIFFRACTION17chain C and (resseq 77:88)
18X-RAY DIFFRACTION18chain C and (resseq 89:100)
19X-RAY DIFFRACTION19chain C and (resseq 101:122)
20X-RAY DIFFRACTION20chain C and (resseq 123:137)
21X-RAY DIFFRACTION21chain D and (resseq 28:41)
22X-RAY DIFFRACTION22chain D and (resseq 42:53)
23X-RAY DIFFRACTION23chain D and (resseq 54:60)
24X-RAY DIFFRACTION24chain D and (resseq 61:67)
25X-RAY DIFFRACTION25chain D and (resseq 68:76)
26X-RAY DIFFRACTION26chain D and (resseq 77:88)
27X-RAY DIFFRACTION27chain D and (resseq 89:100)
28X-RAY DIFFRACTION28chain D and (resseq 101:105)
29X-RAY DIFFRACTION29chain D and (resseq 106:117)
30X-RAY DIFFRACTION30chain D and (resseq 118:122)
31X-RAY DIFFRACTION31chain D and (resseq 123:137)

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