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- PDB-2a79: Mammalian Shaker Kv1.2 potassium channel- beta subunit complex -

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Basic information

Entry
Database: PDB / ID: 2a79
TitleMammalian Shaker Kv1.2 potassium channel- beta subunit complex
Components
  • (poly-unknown ...) x 2
  • Potassium voltage-gated channel subfamily A member 2
  • Voltage-gated potassium channel beta-2 subunit
KeywordsMEMBRANE PROTEIN / potassium channel / voltage sensor / voltage dependent / ion channel / Shaker / eukaryotic / Kv1.2
Function / homology
Function and homology information


optic nerve structural organization / pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / : / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane ...optic nerve structural organization / pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / : / paranodal junction / regulation of circadian sleep/wake cycle, non-REM sleep / potassium ion export across plasma membrane / regulation of protein localization to cell surface / corpus callosum development / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / : / axon initial segment / juxtaparanode region of axon / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / outward rectifier potassium channel activity / myoblast differentiation / regulation of potassium ion transmembrane transport / Neutrophil degranulation / optic nerve development / neuronal cell body membrane / neuromuscular process / regulation of dopamine secretion / lamellipodium membrane / action potential / kinesin binding / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / neuronal action potential / axon terminus / voltage-gated potassium channel complex / sensory perception of pain / potassium ion transmembrane transport / calyx of Held / postsynaptic density membrane / protein homooligomerization / cerebral cortex development / cytoplasmic side of plasma membrane / lamellipodium / presynaptic membrane / perikaryon / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / neuron projection / postsynaptic density / endosome / axon / dendrite / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Mammalian shaker kv1.2 potassium channel- beta subunit complex / Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel ...Mammalian shaker kv1.2 potassium channel- beta subunit complex / Potassium channel, voltage dependent, Kv1.2 / Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / NADP-dependent oxidoreductase domain / Helix Hairpins - #70 / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein / Helix Hairpins / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Voltage-gated potassium channel subunit beta-2 / Potassium voltage-gated channel subfamily A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLong, S.B. / Campbell, E.B. / MacKinnon, R.
Citation
Journal: Science / Year: 2005
Title: Crystal structure of a mammalian voltage-dependent Shaker family K+ channel.
Authors: Long, S.B. / Campbell, E.B. / Mackinnon, R.
#1: Journal: Science / Year: 2005
Title: Voltage Sensor of Kv1.2: Structural Basis of Electromechanical Coupling
Authors: Long, S.B. / Campbell, E.B. / MacKinnon, R.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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_initial_refinement_model / 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
Remark 999SEQUENCE SEE REMARK 3, OTHER REFINEMENT REMARKS, FOR DETAILS REGARDING POLY-UNKNOWN CHAINS C AND D ...SEQUENCE SEE REMARK 3, OTHER REFINEMENT REMARKS, FOR DETAILS REGARDING POLY-UNKNOWN CHAINS C AND D AND THEIR RELATIONSHIP TO CHAIN B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated potassium channel beta-2 subunit
B: Potassium voltage-gated channel subfamily A member 2
C: poly-unknown chain
D: poly-unknown chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,32911
Polymers100,3514
Non-polymers9787
Water1,49583
1
A: Voltage-gated potassium channel beta-2 subunit
B: Potassium voltage-gated channel subfamily A member 2
C: poly-unknown chain
D: poly-unknown chain
hetero molecules

A: Voltage-gated potassium channel beta-2 subunit
B: Potassium voltage-gated channel subfamily A member 2
C: poly-unknown chain
D: poly-unknown chain
hetero molecules

A: Voltage-gated potassium channel beta-2 subunit
B: Potassium voltage-gated channel subfamily A member 2
C: poly-unknown chain
D: poly-unknown chain
hetero molecules

A: Voltage-gated potassium channel beta-2 subunit
B: Potassium voltage-gated channel subfamily A member 2
C: poly-unknown chain
D: poly-unknown chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,31744
Polymers401,40516
Non-polymers3,91228
Water1448
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)113.605, 113.605, 260.473
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
11B-500-

K

21B-501-

K

31B-502-

K

41B-503-

K

51B-504-

K

61B-505-

K

DetailsThe biological unit is a tetramer formed by applying the I4 crystallographic symmetry to the coordinates that are deposited.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Voltage-gated potassium channel beta-2 subunit / K+ / channel beta-2 subunit / Kv-beta-2


Mass: 37353.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnab2, Ckbeta2, Kcnb3 / Production host: Pichia pastoris (fungus) / References: UniProt: P62483
#2: Protein Potassium voltage-gated channel subfamily A member 2 / Voltage-gated potassium channel subunit Kv1.2 / RBK2 / RCK5 / RAK


Mass: 56749.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Pichia pastoris (fungus) / References: UniProt: P63142

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Poly-unknown ... , 2 types, 2 molecules CD

#3: Protein poly-unknown chain


Mass: 4443.468 Da / Num. of mol.: 1 / Fragment: T1-S1 linker and S1 helix of the Kv1.2 channel
Source method: isolated from a genetically manipulated source
Details: Chain C consists of a polyglycine model for the T1-S1 linker and a polyalanine model for the S1 helix of Kv1.2.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Pichia pastoris (fungus)
#4: Protein/peptide poly-unknown chain


Mass: 1805.216 Da / Num. of mol.: 1 / Fragment: S3 helix of the Kv1.2 channel
Source method: isolated from a genetically manipulated source
Details: Chain D consists of a polyalanine model for the S3 helix of Kv1.2.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Production host: Pichia pastoris (fungus)

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Non-polymers , 3 types, 90 molecules

#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.47 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: peg 400, potassium chloride, tris buffer, EDTA, DTT, TCEP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2005 / Details: NSLS X25
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 36056 / Num. obs: 36056 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 2.92 % / Biso Wilson estimate: 60.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3636 / Rsym value: 0.477 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXB

1exb


Resolution: 2.9→29.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4165737.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Some of the missing residues listed in remark 465 are actually the residues that comprise chains C and D. The authors state it is unclear how to align the residues of chains C and D to the ...Details: Some of the missing residues listed in remark 465 are actually the residues that comprise chains C and D. The authors state it is unclear how to align the residues of chains C and D to the sequence of chain B, so each stretch of density assigned chain IDs C and D is labelled as UNK for unknown residue and was modelled in refinement as alanine or glycine.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1776 5.3 %RANDOM
Rwork0.222 ---
all0.224 36056 --
obs0.222 33343 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.2425 Å2 / ksol: 0.295433 e/Å3
Displacement parametersBiso mean: 89.1 Å2
Baniso -1Baniso -2Baniso -3
1--17.57 Å20 Å20 Å2
2---17.57 Å20 Å2
3---35.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 54 83 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.841
X-RAY DIFFRACTIONc_mcangle_it1.491.5
X-RAY DIFFRACTIONc_scbond_it1.21.5
X-RAY DIFFRACTIONc_scangle_it1.911.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.391 162 5.6 %
Rwork0.337 2717 -
obs--79.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3nap.parnap.top
X-RAY DIFFRACTION4ion.paramion.top

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