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- PDB-3lnm: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel -

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Basic information

Entry
Database: PDB / ID: 3lnm
TitleF233W mutant of the Kv2.1 paddle-Kv1.2 chimera channel
Components
  • F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
  • Voltage-gated potassium channel subunit beta-2
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / voltage-gated potassium channel-beta subunit complex / Acetylation / Cytoplasm / Ion transport / Ionic channel / NADP / Phosphoprotein / Potassium / Potassium transport / Transport / Voltage-gated channel / Glycoprotein / Lipoprotein / Membrane / Palmitate / Potassium channel / Transmembrane
Function / homology
Function and homology information


optic nerve structural organization / pinceau fiber / regulation of action potential / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / positive regulation of norepinephrine secretion ...optic nerve structural organization / pinceau fiber / regulation of action potential / clustering of voltage-gated potassium channels / positive regulation of long-term synaptic depression / regulation of motor neuron apoptotic process / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / positive regulation of norepinephrine secretion / NADPH oxidation / positive regulation of catecholamine secretion / paranodal junction / potassium ion export across plasma membrane / proximal dendrite / positive regulation of calcium ion-dependent exocytosis / regulation of circadian sleep/wake cycle, non-REM sleep / cholinergic synapse / axon initial segment / regulation of protein localization to cell surface / delayed rectifier potassium channel activity / corpus callosum development / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / aldo-keto reductase (NADPH) activity / vesicle docking involved in exocytosis / outward rectifier potassium channel activity / juxtaparanode region of axon / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / optic nerve development / postsynaptic specialization membrane / regulation of potassium ion transmembrane transport / glutamate receptor signaling pathway / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / myoblast differentiation / Neutrophil degranulation / response to L-glutamate / neuromuscular process / action potential / neuronal cell body membrane / regulation of dopamine secretion / voltage-gated potassium channel activity / cellular response to nutrient levels / lamellipodium membrane / kinesin binding / neuronal action potential / calyx of Held / positive regulation of protein targeting to membrane / response to axon injury / potassium channel regulator activity / lateral plasma membrane / negative regulation of insulin secretion / hematopoietic progenitor cell differentiation / voltage-gated potassium channel complex / axon terminus / sensory perception of pain / potassium ion transmembrane transport / dendrite membrane / cellular response to calcium ion / extrinsic component of cytoplasmic side of plasma membrane / SNARE binding / protein localization to plasma membrane / cellular response to glucose stimulus / postsynaptic density membrane / sarcolemma / protein homooligomerization / potassium ion transport / cytoplasmic side of plasma membrane / cerebral cortex development / glucose homeostasis / presynaptic membrane / lamellipodium / perikaryon / postsynaptic membrane / transmembrane transporter binding / postsynaptic density / cytoskeleton / endosome / neuron projection / apical plasma membrane / protein heterodimerization activity / axon / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / membrane / plasma membrane / cytosol
Similarity search - Function
Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Potassium channel, voltage dependent, Kv1.2 / Kv2 voltage-gated K+ channel / 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, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv ...Potassium channel, voltage dependent, Kv2.1 / Potassium channel, voltage dependent, Kv2 / Potassium channel, voltage dependent, Kv1.2 / Kv2 voltage-gated K+ channel / 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, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Helix Hairpins - #70 / NADP-dependent oxidoreductase domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / 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 / Potassium voltage-gated channel subfamily B member 1 / 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 / isomorphous to the wild-type structure / Resolution: 2.9 Å
AuthorsTao, X. / Lee, A. / Limapichat, W. / Dougherty, D.A. / MacKinnon, R.
CitationJournal: Science / Year: 2010
Title: A gating charge transfer center in voltage sensors.
Authors: Tao, X. / Lee, A. / Limapichat, W. / Dougherty, D.A. / MacKinnon, R.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 13, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
C: Voltage-gated potassium channel subunit beta-2
D: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,04229
Polymers192,4284
Non-polymers11,61525
Water4,378243
1
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

D: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
hetero molecules

D: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
hetero molecules

D: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
hetero molecules

D: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,60736
Polymers384,8558
Non-polymers6,75228
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
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_564-x,-y+1,z-11
crystal symmetry operation3_554-y+1/2,x+1/2,z-11
crystal symmetry operation4_454y-1/2,-x+1/2,z-11
2
B: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
C: Voltage-gated potassium channel subunit beta-2
hetero molecules

B: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
C: Voltage-gated potassium channel subunit beta-2
hetero molecules

B: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
C: Voltage-gated potassium channel subunit beta-2
hetero molecules

B: F233W mutant of the Kv2.1 paddle-Kv1.2 chimera
C: Voltage-gated potassium channel subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,56380
Polymers384,8558
Non-polymers39,70872
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
Unit cell
Length a, b, c (Å)144.271, 144.271, 284.060
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-501-

K

21B-502-

K

31B-503-

K

41B-504-

K

51B-505-

K

61D-501-

K

71D-502-

K

81D-503-

K

91D-504-

K

101D-505-

K

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Components

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Protein , 2 types, 4 molecules ACBD

#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 / Fragment: subunit beta-2 core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ckbeta2, Kcnab2, Kcnb3 / Plasmid: picZ / Production host: pichia pastoris (fungus) / Strain (production host): SMD1163H / References: UniProt: P62483
#2: Protein F233W mutant of the Kv2.1 paddle-Kv1.2 chimera / Voltage-gated potassium channel subunit Kv1.2 / RBK2 / RCK5 / RAK


Mass: 58860.711 Da / Num. of mol.: 2 / Mutation: C31S, C32S, N207Q, F233W, C431S, C478S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2 / Plasmid: picZ / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163H / References: UniProt: P63142, UniProt: P15387

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Non-polymers , 4 types, 268 molecules

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


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: 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 / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25-28% PEG 400, 50mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 8.3-8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 67020 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 17.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6391

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: isomorphous to the wild-type structure
Starting model: pdb entry 2R9R

2r9r


Resolution: 2.9→49.64 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3407515.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3228 4.8 %RANDOM
Rwork0.211 ---
obs0.211 66928 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.9815 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 71 Å2
Baniso -1Baniso -2Baniso -3
1--6.23 Å20 Å20 Å2
2---6.23 Å20 Å2
3---12.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-4 Å
Luzzati sigma a0.49 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 253 243 11308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.303 293 4.6 %
Rwork0.297 6117 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2nap.parcarbohydrate.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4water_rep.paramion.top
X-RAY DIFFRACTION5pgb_ro10.parnap.top

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