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- PDB-4jtd: Crystal structure of Kv1.2-2.1 paddle chimera channel in complex ... -

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Basic information

Entry
Database: PDB / ID: 4jtd
TitleCrystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin
Components
  • Potassium channel toxin alpha-KTx 1.1
  • Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
  • Voltage-gated potassium channel subunit beta-2
KeywordsTRANSPORT PROTEIN/toxin / potassium channel / pore blocking toxin / protein-protein complex / trans-enhanced dissociation effect / TRANSPORT PROTEIN-toxin complex
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 / ion channel inhibitor activity / 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 / defense response to fungus / 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 / lamellipodium / presynaptic membrane / toxin activity / perikaryon / postsynaptic membrane / killing of cells of another organism / transmembrane transporter binding / postsynaptic density / cytoskeleton / endosome / neuron projection / defense response to bacterium / 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 / extracellular region / 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 / Scorpion short toxins signature. ...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 / Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / 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 / Knottin, scorpion toxin-like superfamily / 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 channel toxin alpha-KTx 1.1 / 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)
Leiurus quinquestriatus hebraeus (scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsBanerjee, A. / Lee, A. / Campbell, E. / MacKinnon, R.
CitationJournal: Elife / Year: 2013
Title: Structure of a pore-blocking toxin in complex with a eukaryotic voltage-dependent K(+) channel.
Authors: Banerjee, A. / Lee, A. / Campbell, E. / Mackinnon, R.
History
DepositionMar 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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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: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
Y: Potassium channel toxin alpha-KTx 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,19432
Polymers196,6625
Non-polymers14,53327
Water5,639313
1
A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
hetero molecules

A: Voltage-gated potassium channel subunit beta-2
B: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 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
2
G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
hetero molecules

G: Voltage-gated potassium channel subunit beta-2
H: Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1
Y: Potassium channel toxin alpha-KTx 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,60633
Polymers389,0119
Non-polymers6,59524
Water1448
TypeNameSymmetry operationNumber
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
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.867, 144.867, 284.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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

51H-501-

K

61H-502-

K

71H-503-

K

81H-504-

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: Ckbeta2, Kcnab2, Kcnb3 / Production host: Pichia pastoris (fungus) / References: UniProt: P62483
#2: Protein Potassium voltage-gated channel subfamily A member 2, Potassium voltage-gated channel subfamily B member 1 / RAK / RBK2 / RCK5 / Voltage-gated potassium channel subunit Kv1.2 / Delayed rectifier potassium ...RAK / RBK2 / RCK5 / Voltage-gated potassium channel subunit Kv1.2 / Delayed rectifier potassium channel 1 / DRK1 / Voltage-gated potassium channel subunit Kv2.1


Mass: 58821.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a chimeric channel between Kv1.2 and Kv2.1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcna2, Kcnb1 / Production host: Pichia pastoris (fungus) / References: UniProt: P63142, UniProt: P15387

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Protein/peptide , 1 types, 1 molecules Y

#3: Protein/peptide Potassium channel toxin alpha-KTx 1.1 / ChTX-Lq1 / ChTx-a / Charybdotoxin / ChTX


Mass: 4312.013 Da / Num. of mol.: 1 / Fragment: Charybdotoxin / Mutation: K27M
Source method: isolated from a genetically manipulated source
Details: K27M mutant
Source: (gene. exp.) Leiurus quinquestriatus hebraeus (scorpion)
Production host: Escherichia coli (E. coli) / References: UniProt: P13487

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Non-polymers , 4 types, 340 molecules

#4: 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
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: 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.: 17 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsONE CHANNEL TETRAMER (GENERATED BY USING THE BIOMT TRANSFORMATIONS ON CHAINS G AND H AS NOTED ABOVE) ...ONE CHANNEL TETRAMER (GENERATED BY USING THE BIOMT TRANSFORMATIONS ON CHAINS G AND H AS NOTED ABOVE) BINDS TO ONE MOLECULE OF TOXIN (CHAIN Y). THE TOXIN CAN BIND IN FOUR DISTINCT ORIENTATIONS ALL OF WHICH ARE PARTIALLY OCCUPIED IN THE LATTICE. THE TOXIN WAS REFINED WITH 1/4 OCCUPANCY WITH ONE ORIENTATION OF THE TOXIN IN THE ASYMMETRIC UNIT. THE SYMMETRY OPERATIONS AROUND THE 4 FOLD SYMMETRY AXIS GENERATES THE OTHER POSSIBLE THREE ORIENTATIONS. PLEASE SEE PRIMARY CITATION FOR MORE DETAILS.
Sequence detailsPROTEIN IN CHAINS B,H IS A CHIMERIC PROTEIN OF RAT KV1.2 AND RAT KV2.1. PLEASE REFER TO THE PRIMARY ...PROTEIN IN CHAINS B,H 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 97913 / % possible obs: 96.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.104 / Χ2: 1.077 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.54-2.5860.80916261.041132.8
2.58-2.637.30.7850181.0481100
2.63-2.687.30.68149801.0861100
2.68-2.747.30.62149971.0761100
2.74-2.87.30.51950021.0921100
2.8-2.867.40.40849951.0991100
2.86-2.937.40.32949931.0961100
2.93-3.017.40.27850151.0841100
3.01-3.17.40.22650071.0931100
3.1-3.27.40.18950171.0661100
3.2-3.317.40.15550561.0521100
3.31-3.457.40.12550431.0761100
3.45-3.67.40.10850311.081100
3.6-3.797.30.09150421.0441100
3.79-4.037.30.08150921.0421100
4.03-4.347.30.07650751.081100
4.34-4.787.20.07551191.0981100
4.78-5.477.20.08251451.1261100
5.47-6.8970.07652191.0251100
6.89-506.80.06254411.106199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→50 Å / Occupancy max: 1 / Occupancy min: 0.25 / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THERE IS A TOXIN MOLECULE BOUND TO THE CHANNEL TETRAMER GENERATED BY FOUR COPIES OF A TOGETHER WITH FOUR COPIES OF B. HOWEVER IT WAS NOT BUILT BECAUSE IT WAS NOT SUFFICIENTLY WELL ORDERED. ...Details: THERE IS A TOXIN MOLECULE BOUND TO THE CHANNEL TETRAMER GENERATED BY FOUR COPIES OF A TOGETHER WITH FOUR COPIES OF B. HOWEVER IT WAS NOT BUILT BECAUSE IT WAS NOT SUFFICIENTLY WELL ORDERED. RESIDUES 133-144 IN CHAIN B WAS BUILT AS A POLYGLYCINE CHAIN BECAUSE OF LACK OF ADEQUATE ELECTRON DENSITY FOR THE SIDE CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 4406 4.4 %random
Rwork0.21 ---
all-100265 --
obs-93308 93.1 %-
Solvent computationBsol: 64.2602 Å2
Displacement parametersBiso max: 202.68 Å2 / Biso mean: 74.5196 Å2 / Biso min: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.563 Å20 Å20 Å2
2---5.563 Å20 Å2
3---11.127 Å2
Refinement stepCycle: LAST / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11453 0 316 313 12082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.245
X-RAY DIFFRACTIONc_mcbond_it1.2431.5
X-RAY DIFFRACTIONc_scbond_it2.1252
X-RAY DIFFRACTIONc_mcangle_it2.1052
X-RAY DIFFRACTIONc_scangle_it3.1752.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.630.26732490.26626257650665.8
2.63-2.740.30693950.26578371876688.8
2.74-2.860.30694230.24488640906391.8
2.86-3.010.2614450.21758855930093.6
3.01-3.20.25434230.21849103952696.1
3.2-3.450.22284870.20429257974497.6
3.45-3.790.21664890.19469367985698.7
3.79-4.340.20984880.18339480996899.2
4.34-5.470.21155080.186295931010199.3
5.47-500.010.24774990.231999791047898.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION6nap_par.txtnap_top.txt
X-RAY DIFFRACTION7pgb_ro10.parpgb.top
X-RAY DIFFRACTION8pca.parpca.top

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