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- PDB-1r3k: potassium channel KcsA-Fab complex in low concentration of Tl+ -

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Basic information

Entry
Database: PDB / ID: 1r3k
Titlepotassium channel KcsA-Fab complex in low concentration of Tl+
Components
  • Antibody Fab fragment heavy chain
  • Antibody Fab fragment light chain
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / potassium channel / KcsA-Fab complex / Thallium
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / voltage-gated potassium channel activity / immunoglobulin mediated immune response ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / voltage-gated potassium channel activity / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / : / Helix Hairpins / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / : / Helix Hairpins / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DIACYL GLYCEROL / THALLIUM (I) ION / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhou, Y. / MacKinnon, R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The occupancy of ions in the K+ selectivity filter: Charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates
Authors: Zhou, Y. / MacKinnon, R.
History
DepositionOct 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN The ligand DGA is a partial lipid.
Remark 999SEQUENCE A suitable database reference sequence could not be found for chains A and B at the time ...SEQUENCE A suitable database reference sequence could not be found for chains A and B at the time of processing.

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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)61,2977
Polymers60,0593
Non-polymers1,2384
Water00
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)245,18728
Polymers240,23412
Non-polymers4,95316
Water0
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
Unit cell
Length a, b, c (Å)154.180, 154.180, 75.050
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-301-

TL

21C-302-

TL

31C-303-

TL

Detailshomo-tetramer of KcsA is generated by four fold axis: x,y,z -x,-y,z -x,y,z x,-y,z

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Components

#1: Antibody Antibody Fab fragment light chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody Antibody Fab fragment heavy chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS
#3: Protein Voltage-gated potassium channel


Mass: 13211.582 Da / Num. of mol.: 1 / Mutation: P2A,L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: KCSA, SKC1, SCO7660, SC10F4.33 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: P0A334
#4: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#5: Chemical ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tl
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: 66.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: PEG400, sodium acetate, magnesium acetate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris1droppH7.5
25 mMDM1drop
325 mM1dropTlNO3
418-25 %(w/v)PEG4001reservoir
550 mMmagnesium acetate1reservoir
650 mMsodium acetate1reservoirpH5.4
7215 mM1dropNaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 21868 / Num. obs: 21868 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 2.8→29.74 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The occupancy of ions in this model were estimated values. Please refer to the primary citation for a detailed analysis of ion occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1094 5 %RANDOM
Rwork0.238 ---
all0.24 21821 --
obs0.24 21821 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5527 Å2 / ksol: 0.347237 e/Å3
Displacement parametersBiso mean: 61.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.37 Å20 Å20 Å2
2---5.37 Å20 Å2
3---10.74 Å2
Refine analyzeLuzzati coordinate error free: 0.46 Å / Luzzati sigma a free: 0.59 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 24 0 4005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 172 4.8 %
Rwork0.351 3403 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TL_PB.PARLIPID.TOP
X-RAY DIFFRACTION4LIPID.PARTL_CHARGE.TOP
Software
*PLUS
Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93

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