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- PDB-3f5w: KcsA Potassium channel in the open-inactivated state with 32 A op... -

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Basic information

Entry
Database: PDB / ID: 3f5w
TitleKcsA Potassium channel in the open-inactivated state with 32 A opening at T112
Components
  • Antibody heavy chainImmunoglobulin heavy chain
  • Antibody light chainImmunoglobulin light chain
  • Voltage-gated potassium channel
Keywordsmembrane protein/metal transport / Potassium channel / KcsA / Open / Inactivated / Cell membrane / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel / membrane protein-metal transport COMPLEX
Function / homology
Function and homology information


monoatomic ion transmembrane transport / 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
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsCuello, L.G. / Jogini, V. / Cortes, D.M. / Perozo, E.
CitationJournal: TO BE PUBLISHED
Title: KcsA Potassium channel in the open-inactivated state with 32 A opening at T112
Authors: Cuello, L.G. / Jogini, V. / Cortes, D.M. / Perozo, E.
History
DepositionNov 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2018Group: Advisory / Data collection ...Advisory / Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_distant_solvent_atoms
Item: _entity.src_method
Revision 1.3Oct 20, 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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody heavy chain
B: Antibody light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8535
Polymers57,7753
Non-polymers782
Water362
1
A: Antibody heavy chain
B: Antibody light chain
C: Voltage-gated potassium channel
hetero molecules

A: Antibody heavy chain
B: Antibody light chain
C: Voltage-gated potassium channel
hetero molecules

A: Antibody heavy chain
B: Antibody light chain
C: Voltage-gated potassium channel
hetero molecules

A: Antibody heavy chain
B: Antibody light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,41120
Polymers231,09812
Non-polymers3138
Water724
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 area27970 Å2
ΔGint-157 kcal/mol
Surface area86000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.860, 155.860, 73.115
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-1-

K

21C-2-

K

31C-125-

HOH

41C-126-

HOH

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Components

#1: Antibody Antibody heavy chain / Immunoglobulin heavy chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody light chain / Immunoglobulin light chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Voltage-gated potassium channel /


Mass: 10927.571 Da / Num. of mol.: 1 / Mutation: H25Q,L90C,R117Q,E120Q,R121Q,R122Q,H124Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG 400, 50 mM Sodium acetate, 50mM magnesium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→40 Å / Num. all: 13379 / Num. obs: 12767 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.23→3.38 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 3.3→40 Å / Occupancy max: 1 / Occupancy min: 0.25 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.265 1298 9.7 %
Rwork0.259 11469 -
obs-12767 95.4 %
Solvent computationBsol: 45.683 Å2
Displacement parametersBiso max: 163.69 Å2 / Biso mean: 102.739 Å2 / Biso min: 37.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.352 Å20 Å20 Å2
2---4.352 Å20 Å2
3---8.703 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 2 2 3924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d1.463

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