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- PDB-4gx5: GsuK Channel -

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Basic information

Entry
Database: PDB / ID: 4gx5
TitleGsuK Channel
ComponentsTrkA domain protein
KeywordsTRANSPORT PROTEIN / Membrane Protein / Ion Channel / ADP binding / NAD binding / Membrane
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / nucleotide binding / membrane / metal ion binding
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain ...Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / TrkA domain protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsKong, C. / Zeng, W. / Ye, S. / Chen, L. / Sauer, D.B. / Lam, Y. / Derebe, M.G. / Jiang, Y.
CitationJournal: elife / Year: 2012
Title: Distinct gating mechanisms revealed by the structures of a multi-ligand gated K(+) channel.
Authors: Kong, C. / Zeng, W. / Ye, S. / Chen, L. / Sauer, D.B. / Lam, Y. / Derebe, M.G. / Jiang, Y.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: TrkA domain protein
B: TrkA domain protein
C: TrkA domain protein
D: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,21224
Polymers247,3214
Non-polymers89120
Water0
1
A: TrkA domain protein
B: TrkA domain protein
hetero molecules

A: TrkA domain protein
B: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,21224
Polymers247,3214
Non-polymers89120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13540 Å2
ΔGint-113 kcal/mol
Surface area80500 Å2
MethodPISA
2
C: TrkA domain protein
D: TrkA domain protein
hetero molecules

C: TrkA domain protein
D: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,21224
Polymers247,3214
Non-polymers89120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area13700 Å2
ΔGint-115 kcal/mol
Surface area80330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.976, 108.364, 165.787
Angle α, β, γ (deg.)90.00, 134.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-601-

K

21A-602-

K

31A-603-

K

41A-604-

K

51A-607-

K

61A-608-

K

71C-601-

K

81C-602-

K

91C-603-

K

101C-604-

K

111C-608-

K

121C-609-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 19:109 or resseq 111:260 or resseq 351:480 )
21chain B and (resseq 19:109 or resseq 111:260 or resseq 351:480 )
31chain C and (resseq 19:109 or resseq 111:260 or resseq 351:480 )
41chain D and (resseq 19:109 or resseq 111:260 or resseq 351:480 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUchain 'A' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )AA19 - 10916 - 106
12PROPROTHRTHRchain 'A' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )AA111 - 260108 - 257
13ASPASPLYSLYSchain 'A' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )AA351 - 480348 - 477
21ASNASNLEULEUchain 'B' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )BB19 - 10916 - 106
22PROPROTHRTHRchain 'B' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )BB111 - 260108 - 257
23ASPASPLYSLYSchain 'B' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )BB351 - 480348 - 477
31ASNASNLEULEUchain 'C' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )CC19 - 10916 - 106
32PROPROTHRTHRchain 'C' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )CC111 - 260108 - 257
33ASPASPLYSLYSchain 'C' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )CC351 - 480348 - 477
41ASNASNLEULEUchain 'D' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )DD19 - 10916 - 106
42PROPROTHRTHRchain 'D' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )DD111 - 260108 - 257
43ASPASPLYSLYSchain 'D' and (resseq 19:109 or resseq 111:260 or resseq 351:480 )DD351 - 480348 - 477

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Components

#1: Protein
TrkA domain protein


Mass: 61830.309 Da / Num. of mol.: 4 / Mutation: E52A, Q77E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: GSU0527 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q74FS9
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 13-18% PEG 3350, 250-500mM KSCN, 100mM CHES, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 27539 / % possible obs: 86.7 % / Observed criterion σ(I): 0.902
Reflection shellResolution: 3.7→3.76 Å / % possible all: 47.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→45.393 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 38.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2929 1382 5.03 %Random
Rwork0.2605 ---
obs0.2623 27458 86.76 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 162.069 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7228 Å20 Å235.7441 Å2
2---20.1721 Å20 Å2
3---24.8948 Å2
Refinement stepCycle: LAST / Resolution: 3.7→45.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14246 0 20 0 14266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614532
X-RAY DIFFRACTIONf_angle_d1.05319788
X-RAY DIFFRACTIONf_dihedral_angle_d16.5875212
X-RAY DIFFRACTIONf_chiral_restr0.0652365
X-RAY DIFFRACTIONf_plane_restr0.0042527
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2892X-RAY DIFFRACTIONPOSITIONAL0.073
12B2892X-RAY DIFFRACTIONPOSITIONAL0.073
13C2892X-RAY DIFFRACTIONPOSITIONAL0.048
14D2892X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.83230.4203830.35781518X-RAY DIFFRACTION51
3.8323-3.98560.3802990.35121958X-RAY DIFFRACTION66
3.9856-4.16690.34521010.33052411X-RAY DIFFRACTION79
4.1669-4.38640.30981330.30142570X-RAY DIFFRACTION87
4.3864-4.6610.31871320.26392842X-RAY DIFFRACTION95
4.661-5.02040.25481680.23742959X-RAY DIFFRACTION99
5.0204-5.52490.31911400.25242974X-RAY DIFFRACTION99
5.5249-6.32250.28721550.25912979X-RAY DIFFRACTION99
6.3225-7.95870.28631830.23132978X-RAY DIFFRACTION99
7.9587-45.39630.27741880.25112887X-RAY DIFFRACTION95
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)
18.24860.8722-1.41872.66441.30187.9572-0.11950.08270.9646-0.03220.4243-0.8813-0.59270.363-0.36251.6549-0.08950.01311.02190.03771.166-49.176-46.936960.1412
25.10580.8044-1.62695.25882.07476.8260.3844-0.07861.62790.17670.3185-0.5376-0.45170.5111-0.39511.0715-0.25330.17021.1814-0.04632.0811-108.0075-20.1203118.9765
32.74030.0434-1.8537.4517-0.86358.38210.11550.46760.17750.41870.36931.15180.10480.0666-0.29290.82660.1063-0.0261.12730.12961.3285-32.744811.284959.7713
48.3823-2.12353.24981.14380.01913.8717-0.51220.5512-1.6568-0.2759-0.10770.42850.1759-0.41850.40931.5838-0.42940.48961.5083-0.14771.4624-57.474411.238633.3616
54.8287-2.0469-2.19534.1088-0.5958.47780.42570.5021-0.1324-0.6529-0.2238-0.89321.11660.5418-0.00670.8539-0.0908-0.35951.3763-0.23761.2523-91.80738.2093119.0884
67.11770.6099-0.03074.6317-2.3423.2128-0.2509-0.0973-0.33620.30880.32320.0467-0.5407-0.1756-0.20411.470.24650.14171.3913-0.1031.0547-115.448438.165891.4855
73.26362.16270.47044.64493.13764.71090.15160.2924-0.9044-1.86660.4594-1.8243-0.00391.1726-0.71953.0716-1.35460.1682.1646-0.24851.5218-55.977812.77534.1456
83.4356-3.2646-0.86753.94112.24352.6686-0.5387-1.40342.12811.48610.4832-0.6599-0.87190.47660.57561.4133-0.23-0.08332.4276-0.53652.7616-62.629739.5326120.9481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:119 ) OR ( CHAIN B AND RESID 17:119 )A18 - 119
2X-RAY DIFFRACTION1( CHAIN A AND RESID 18:119 ) OR ( CHAIN B AND RESID 17:119 )B17 - 119
3X-RAY DIFFRACTION2( CHAIN C AND RESID 19:119 ) OR ( CHAIN D AND RESID 18:119 )C19 - 119
4X-RAY DIFFRACTION2( CHAIN C AND RESID 19:119 ) OR ( CHAIN D AND RESID 18:119 )D18 - 119
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 120:261 OR RESID 350:480 OR RESID 605:605 ) )A120 - 261
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 120:261 OR RESID 350:480 OR RESID 605:605 ) )A350 - 480
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 120:261 OR RESID 350:480 OR RESID 605:605 ) )A605
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 120:260 OR RESID 350:480 OR RESID 601:601 ) )B120 - 260
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 120:260 OR RESID 350:480 OR RESID 601:601 ) )B350 - 480
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 120:260 OR RESID 350:480 OR RESID 601:601 ) )B601
11X-RAY DIFFRACTION5( CHAIN C AND ( RESID 120:261 OR RESID 351:482 OR RESID 605:605 ) )C120 - 261
12X-RAY DIFFRACTION5( CHAIN C AND ( RESID 120:261 OR RESID 351:482 OR RESID 605:605 ) )C351 - 482
13X-RAY DIFFRACTION5( CHAIN C AND ( RESID 120:261 OR RESID 351:482 OR RESID 605:605 ) )C605
14X-RAY DIFFRACTION6( CHAIN D AND ( RESID 120:261 OR RESID 351:482 OR RESID 601:601 ) )D120 - 261
15X-RAY DIFFRACTION6( CHAIN D AND ( RESID 120:261 OR RESID 351:482 OR RESID 601:601 ) )D351 - 482
16X-RAY DIFFRACTION6( CHAIN D AND ( RESID 120:261 OR RESID 351:482 OR RESID 601:601 ) )D601
17X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B261 - 349
18X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B481 - 564
19X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C262 - 350
20X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C483 - 564

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