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- PDB-2r9r: Shaker family voltage dependent potassium channel (kv1.2-kv2.1 pa... -

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Basic information

Entry
Database: PDB / ID: 2r9r
TitleShaker family voltage dependent potassium channel (kv1.2-kv2.1 paddle chimera channel) in association with beta subunit
Components
  • Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
  • Voltage-gated potassium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / POTASSIUM CHANNEL / VOLTAGE SENSOR / VOLTAGE DEPENDENT / ION CHANNEL / SHAKER / EUKARYOTIC / KV1.2 / KV2.1 / PADDLE CHIMERA CHANNEL / Ion transport / Ionic channel / NADP / Phosphorylation / Potassium transport / Transport / Voltage-gated channel / PROTEIN TRANSPORT
Function / homology
Function and homology information


pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / regulation of protein localization to cell surface / : / axon initial segment / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / myoblast differentiation ...pinceau fiber / methylglyoxal reductase (NADPH) (acetol producing) activity / Voltage gated Potassium channels / potassium channel complex / regulation of protein localization to cell surface / : / axon initial segment / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / juxtaparanode region of axon / myoblast differentiation / regulation of potassium ion transmembrane transport / Neutrophil degranulation / neuromuscular process / voltage-gated potassium channel activity / potassium channel regulator activity / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / postsynaptic density membrane / cytoplasmic side of plasma membrane / transmembrane transporter binding / cytoskeleton / neuron projection / postsynaptic density / axon / protein-containing complex binding / glutamatergic synapse / membrane / cytosol
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Voltage-gated potassium channels. Chain C / 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 ...Potassium channel, voltage-dependent, beta subunit, KCNAB2 / Potassium channel, voltage-dependent, beta subunit, KCNAB / Potassium channel, voltage-dependent, beta subunit, KCNAB-related / Voltage-gated potassium channels. Chain C / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix Hairpins / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-PGW / Voltage-gated potassium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLong, S.B. / Tao, X. / Campbell, E.B. / Mackinnon, R.
Citation
Journal: Nature / Year: 2007
Title: Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment.
Authors: Long, S.B. / Tao, X. / Campbell, E.B. / MacKinnon, R.
#1: 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.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_ref_seq / struct_ref_seq_dif
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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Remark 999sequence sequence of chain B,H has not exact UNP database match. It is a chimeric protein of rat ...sequence sequence of chain B,H has not exact UNP database match. It is a chimeric protein of rat Kv1.2 and rat Kv2.1. Please refer to the primary citation for more details.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,88231
Polymers192,3504
Non-polymers14,53327
Water5,747319
1
A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,23592
Polymers384,6998
Non-polymers51,53684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area66240 Å2
ΔGint106 kcal/mol
Surface area116100 Å2
MethodPISA
2
G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,29432
Polymers384,6998
Non-polymers6,59524
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area38250 Å2
ΔGint-140 kcal/mol
Surface area114460 Å2
MethodPISA
3
A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
G: Voltage-gated potassium channel subunit beta-2
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)827,529124
Polymers769,39816
Non-polymers58,131108
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area107620 Å2
ΔGint-46 kcal/mol
Surface area227430 Å2
MethodPISA
4
A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,3868
Polymers149,4124
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
MethodPQS
5
B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

B: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,84984
Polymers235,2874
Non-polymers48,56280
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
MethodPQS
6
G: Voltage-gated potassium channel subunit beta-2
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,3868
Polymers149,4124
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
MethodPQS
7
H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules

H: Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,90824
Polymers235,2874
Non-polymers3,62220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.049, 144.049, 284.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-496-

K

21B-497-

K

31B-498-

K

41B-499-

K

51H-496-

K

61H-497-

K

71H-498-

K

81H-499-

K

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Components

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Protein , 2 types, 4 molecules AGBH

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


Mass: 37353.086 Da / Num. of mol.: 2
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 Paddle chimera voltage gated potassium channel Kv1.2-Kv2.1


Mass: 58821.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: kcna2 / Production host: Pichia pastoris (fungus)

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Non-polymers , 4 types, 346 molecules

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


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.83 Å3/Da / Density % sol: 67.93 %
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 293.0K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 112726 / Num. obs: 112726 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 2.47 % / Biso Wilson estimate: 44.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 9974 / Rsym value: 0.436 / % possible all: 86.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2A79

2a79


Resolution: 2.4→49.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5699592.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5319 5.1 %RANDOM
Rwork0.212 ---
all0.214 112726 --
obs0.212 104891 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3798 Å2 / ksol: 0.341816 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.83 Å20 Å20 Å2
2---4.83 Å20 Å2
3---9.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11159 0 336 319 11814
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.951
X-RAY DIFFRACTIONc_mcangle_it1.681.5
X-RAY DIFFRACTIONc_scbond_it1.381.5
X-RAY DIFFRACTIONc_scangle_it2.11.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.292 395 4.8 %
Rwork0.289 7770 -
obs--70.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3nana
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5POPG_pgPOPG_pg

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