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- PDB-3kvt: TETRAMERIZATION DOMAIN FROM AKV3.1 (SHAW-SUBFAMILY) VOLTAGE-GATED... -

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Basic information

Entry
Database: PDB / ID: 3kvt
TitleTETRAMERIZATION DOMAIN FROM AKV3.1 (SHAW-SUBFAMILY) VOLTAGE-GATED POTASSIUM CHANNEL
ComponentsPOTASSIUM CHANNEL PROTEIN SHAW
KeywordsPOTASSIUM CHANNEL / TETRAMERIZATION DOMAIN / MOLECULAR RECOGNITION / ZINC-BINDING
Function / homology
Function and homology information


delayed rectifier potassium channel activity / neuronal cell body membrane / action potential / voltage-gated potassium channel complex / dendrite membrane / axon terminus / protein homooligomerization / presynaptic membrane / postsynaptic membrane / metal ion binding
Similarity search - Function
Potassium channel, voltage dependent, Kv3 / 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 / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily ...Potassium channel, voltage dependent, Kv3 / 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 / 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
Shaw potassium channel Kv3.1a
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBixby, K.A. / Nanao, M.H. / Shen, N.V. / Kreusch, A. / Bellamy, H. / Pfaffinger, P.J. / Choe, S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels.
Authors: Bixby, K.A. / Nanao, M.H. / Shen, N.V. / Kreusch, A. / Bellamy, H. / Pfaffinger, P.J. / Choe, S.
History
DepositionSep 25, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POTASSIUM CHANNEL PROTEIN SHAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4552
Polymers13,3891
Non-polymers651
Water1,20767
1
A: POTASSIUM CHANNEL PROTEIN SHAW
hetero molecules

A: POTASSIUM CHANNEL PROTEIN SHAW
hetero molecules

A: POTASSIUM CHANNEL PROTEIN SHAW
hetero molecules

A: POTASSIUM CHANNEL PROTEIN SHAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8188
Polymers53,5574
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area6480 Å2
ΔGint-173 kcal/mol
Surface area18350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.191, 67.191, 138.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein POTASSIUM CHANNEL PROTEIN SHAW


Mass: 13389.151 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION (T1) DOMAIN / Mutation: A42G, L43M, A44L
Source method: isolated from a genetically manipulated source
Details: ONE ZN2+ PER MONOMER TETRAHEDRALLY COORDINATED AT MONOMER-MONOMER INTERFACE
Source: (gene. exp.) Aplysia californica (California sea hare)
Tissue: NERVE / Cell line: BL21 PLYS S / Cellular location: MEMBRANE / Plasmid: PET16B / Cell line (production host): BL21 PLYS S / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: O76457
#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.: 67 / 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: 2.66 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.5 Msodium formate1reservoir
20.1 Mbis-Tris-propane1reservoir
30.2 M1reservoirMgCl2
40.15 M1reservoirNaCl
510 mMbeta-mercaptoethanol1reservoir
624 %isopropanol1drop
70.2 M1dropMgCl2
80.1 MHEPES1droppH7.5
91 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: PLATINUM COATED MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 11135 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.057
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.401 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 126110 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.401

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AP61

Resolution: 2→25 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 577 5.2 %RANDOM
Rwork0.225 ---
obs0.225 11134 99.7 %-
Displacement parametersBiso mean: 28.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 1 67 902
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.09
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it2.82
X-RAY DIFFRACTIONx_scbond_it2.872
X-RAY DIFFRACTIONx_scangle_it4.432.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 63 5.9 %
Rwork0.286 1012 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM21.IONTOPH21.ION
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.09

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