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- PDB-1nn7: Crystal Structure Of The Tetramerization Domain Of The Shal Volta... -

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Basic information

Entry
Database: PDB / ID: 1nn7
TitleCrystal Structure Of The Tetramerization Domain Of The Shal Voltage-Gated Potassium Channel
Componentspotassium channel Kv4.2
KeywordsMEMBRANE PROTEIN / T1 / teteramerization domain / voltage gated potassium channel / Kv4.2 / shal
Function / homology
Function and homology information


Phase 1 - inactivation of fast Na+ channels / cardiac muscle cell action potential / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / perinuclear endoplasmic reticulum / membrane repolarization / postsynaptic specialization membrane ...Phase 1 - inactivation of fast Na+ channels / cardiac muscle cell action potential / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Voltage gated Potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium channel complex / perinuclear endoplasmic reticulum / membrane repolarization / postsynaptic specialization membrane / anchoring junction / action potential / neuronal cell body membrane / voltage-gated potassium channel activity / potassium channel activity / plasma membrane raft / locomotor rhythm / GABA-ergic synapse / neuronal action potential / potassium ion transmembrane transport / voltage-gated potassium channel complex / sensory perception of pain / T-tubule / caveola / muscle contraction / potassium ion transport / protein homooligomerization / sarcolemma / cellular response to mechanical stimulus / cellular response to xenobiotic stimulus / monoatomic ion channel activity / cellular response to hypoxia / postsynaptic membrane / perikaryon / dendritic spine / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv4.2 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Potassium Channel Kv1.1; Chain A ...Potassium channel, voltage dependent, Kv4.2 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily D member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhou, W. / Choe, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Determining the basis of channel-tetramerization specificity by x-ray crystallography and a sequence-comparison algorithm: Family values (FamVal)
Authors: Nanao, M.H. / Zhou, W. / Pfaffinger, P.J. / Choe, S.
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: potassium channel Kv4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8512
Polymers12,7851
Non-polymers651
Water1,02757
1
A: potassium channel Kv4.2
hetero molecules

A: potassium channel Kv4.2
hetero molecules

A: potassium channel Kv4.2
hetero molecules

A: potassium channel Kv4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4028
Polymers51,1414
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area6450 Å2
ΔGint-170 kcal/mol
Surface area19870 Å2
MethodPISA
2
A: potassium channel Kv4.2
hetero molecules

A: potassium channel Kv4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7014
Polymers25,5702
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)59.999, 59.999, 61.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a tetramer genereated from the monomer in the asymmetric unit by the operations: y-1/2,-x+3/2,z, 1-x,2-y,z and 3/2-y,1/2+x,z

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Components

#1: Protein potassium channel Kv4.2 / Shal Voltage-Gated Potassium Channel


Mass: 12785.146 Da / Num. of mol.: 1
Fragment: N-terminal domain (residues 42-146), tetramerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnd2 / Plasmid: pHIS8(modified pET28) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q63881
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Magnesium chloride, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
25 mMHEPES1droppH7.5
30.1 MTris-HCl1reservoirpH8.5
40.2 M1reservoirMgCl2
55 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 19, 2000
RadiationMonochromator: double-mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. all: 7071 / Num. obs: 7033 / % possible obs: 99.46 % / Redundancy: 8.74 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.055 / Net I/σ(I): 41.54
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 7.55 / Num. unique all: 658 / Rsym value: 0.216 / % possible all: 97
Reflection
*PLUS
Num. obs: 7071 / % possible obs: 99.5 % / Num. measured all: 163537 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly-serine model of PDB entry 3KVT

3kvt


Resolution: 2.1→27.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 753 -RANDOM
Rwork0.23 ---
all-6851 --
obs-6851 100 %-
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.644 Å20 Å20 Å2
2--0.644 Å20 Å2
3----1.289 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.351 Å0.273 Å
Luzzati sigma a0.2618 Å0.1925 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 1 57 945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22594
X-RAY DIFFRACTIONc_bond_d0.005727
X-RAY DIFFRACTIONc_mcbond_it1.319
X-RAY DIFFRACTIONc_mcangle_it2.113
LS refinement shellResolution: 2.1→2.15 Å
RfactorNum. reflection% reflection
Rfree0.3548 43 -
Rwork0.2598 --
obs-426 100 %
Refinement
*PLUS
% reflection Rfree: 10.8 % / Rfactor Rwork: 0.2304
Solvent computation
*PLUS
Displacement parameters
*PLUS

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