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- PDB-2dwd: crystal structure of KcsA-FAB-TBA complex in Tl+ -

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Basic information

Entry
Database: PDB / ID: 2dwd
Titlecrystal structure of KcsA-FAB-TBA complex in Tl+
Components
  • (ANTIBODY FAB ...) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / potassium channel / tetrabutylammonium / K+ / KcsA
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / 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 / (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE / TETRABUTYLAMMONIUM ION / THALLIUM (I) ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYohannan, S. / Zhou, Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic Study of the Tetrabutylammonium Block to the KcsA K(+) Channel
Authors: Yohannan, S. / Hu, Y. / Zhou, Y.
History
DepositionAug 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIBODY FAB HEAVY CHAIN
B: ANTIBODY FAB LIGHT CHAIN
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,44510
Polymers57,8263
Non-polymers1,6197
Water1,38777
1
A: ANTIBODY FAB HEAVY CHAIN
B: ANTIBODY FAB LIGHT CHAIN
C: Voltage-gated potassium channel
hetero molecules

A: ANTIBODY FAB HEAVY CHAIN
B: ANTIBODY FAB LIGHT CHAIN
C: Voltage-gated potassium channel
hetero molecules

A: ANTIBODY FAB HEAVY CHAIN
B: ANTIBODY FAB LIGHT CHAIN
C: Voltage-gated potassium channel
hetero molecules

A: ANTIBODY FAB HEAVY CHAIN
B: ANTIBODY FAB LIGHT CHAIN
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,77840
Polymers231,30312
Non-polymers6,47528
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area36570 Å2
ΔGint-190 kcal/mol
Surface area83910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.18, 153.18, 75.483
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-3001-

TL

21C-3002-

TL

31C-3003-

TL

41C-3004-

TL

51C-4001-

TBA

DetailsBiological assembly is a tetramer generated by: chain A, chain B (x,y,z (1_555),2-x,2-y,z (2_775),2-y,x,z (3_755),y,2-x,z (4_575)), chain C (x,y,z (1_555),2-x,2-y,z (2_775),2-y,x,z (3_755),y,2-x,z (4_575)).

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Components

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Protein , 1 types, 1 molecules C

#3: Protein Voltage-gated potassium channel


Mass: 10978.736 Da / Num. of mol.: 1 / Fragment: residues 22-124 / Mutation: L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P0A334

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Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY FAB HEAVY CHAIN


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cell line / Source: (natural) Mus musculus (house mouse)
#2: Antibody ANTIBODY FAB LIGHT CHAIN


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cell line / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 5 types, 84 molecules

#4: Chemical ChemComp-F09 / NONAN-1-OL


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Tl
#6: Chemical ChemComp-L2C / (2S)-3-HYDROXY-2-(NONANOYLOXY)PROPYL LAURATE


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


Mass: 242.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36N
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18-25% PEG 400, 50mM MG(AC)2, 50mM NaAc(pH 5) or Na cacodylate(pH 6) or HEPES(pH 7), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2005
RadiationMonochromator: Si(220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.76 Å / Num. all: 27271 / Num. obs: 26479 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / % possible all: 95.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4C

1k4c


Resolution: 2.6→48.76 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 1319 RANDOM
Rwork0.219 --
all0.241 27271 -
obs0.241 26479 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3 Å23 Å20 Å2
2--3 Å20 Å2
3----6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 57 77 4190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3

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