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- PDB-2jk5: Potassium Channel KcsA in complex with Tetrabutylammonium in high K -

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Basic information

Entry
Database: PDB / ID: 2jk5
TitlePotassium Channel KcsA in complex with Tetrabutylammonium in high K
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • VOLTAGE-GATED POTASSIUM CHANNEL
KeywordsIMMUNE SYSTEM/METAL TRANSPORT / IMMUNE SYSTEM-METAL TRANSPORT COMPLEX / QUATERNARY AMMONIUM / PROTEIN-ANTIBODY FAB COMPLEX / IONIC CHANNEL / ION TRANSPORT
Function / homology
Function and homology information


voltage-gated potassium channel activity / identical protein binding / plasma membrane
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / NONAN-1-OL / HEPTANE / : / (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE / TETRABUTYLAMMONIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
STREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLenaeus, M.J. / Focia, P.J. / Wagner, T. / Gross, A.
CitationJournal: Biochemistry / Year: 2014
Title: Structures of Kcsa in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site.
Authors: Lenaeus, M.J. / Burdette, D. / Wagner, T. / Focia, P.J. / Gross, A.
History
DepositionAug 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,28014
Polymers60,0853
Non-polymers1,19511
Water3,675204
1
A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,11956
Polymers240,33812
Non-polymers4,78044
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area36390 Å2
ΔGint-204.5 kcal/mol
Surface area88000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.145, 156.145, 76.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1124-

CO

21C-1125-

K

31C-1126-

K

41C-1127-

K

51C-1128-

K

61C-1129-

K

71C-1130-

K

81C-1133-

TBA

91C-2048-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein VOLTAGE-GATED POTASSIUM CHANNEL / KCSA POTASSIUM CHANNEL


Mass: 13237.618 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY FAB FRAGMENT LIGHT CHAIN


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody ANTIBODY FAB FRAGMENT HEAVY CHAIN


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)

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Non-polymers , 7 types, 215 molecules

#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-F09 / NONAN-1-OL


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#7: Chemical ChemComp-L2C / (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE


Mass: 414.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O5
#8: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION


Mass: 242.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36N
#9: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.8 % / Description: NONE
Crystal growpH: 5.4
Details: 18-25%PEG400, 50 MM SODIUM ACETATE, 50 MM MAGNESIUM ACETATE, pH 5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.977
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35756 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.75 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.27
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0051refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4C WITH SELECTIVITY FILTER AND IONS REMOVED

1k4c


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.809 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SEVERAL DISORDERED REGIONS HAVE BEEN MODELED AS WATER (NEAR TRP B163, CHAIN C22-35, AND THE L2C MOLECULE).
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1790 5 %RANDOM
Rwork0.202 ---
obs0.205 33912 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 70 204 4324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9545891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40323.636165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38515645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8081522
X-RAY DIFFRACTIONr_chiral_restr0.0850.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6381.52714
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17524401
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47631604
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4424.51490
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.47 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 116
Rwork0.268 2468

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