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- PDB-3gj9: crystal structure of TIP-1 in complex with c-terminal of Kir2.3 -

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Basic information

Entry
Database: PDB / ID: 3gj9
Titlecrystal structure of TIP-1 in complex with c-terminal of Kir2.3
Components
  • C-terminal peptide from Inward rectifier potassium channel 4
  • Tax1-binding protein 3
KeywordsSIGNALING PROTEIN / TIP-1 / Kir2.3 / PDZ domain / Cytoplasm / Nucleus / Phosphoprotein / Wnt signaling pathway
Function / homology
Function and homology information


Classical Kir channels / Phase 4 - resting membrane potential / negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / cardiac conduction / inward rectifier potassium channel activity / activation of GTPase activity / regulation of monoatomic ion transmembrane transport / negative regulation of Wnt signaling pathway / potassium ion import across plasma membrane ...Classical Kir channels / Phase 4 - resting membrane potential / negative regulation of protein localization to cell surface / RHO GTPases Activate Rhotekin and Rhophilins / cardiac conduction / inward rectifier potassium channel activity / activation of GTPase activity / regulation of monoatomic ion transmembrane transport / negative regulation of Wnt signaling pathway / potassium ion import across plasma membrane / Rho protein signal transduction / voltage-gated potassium channel complex / PDZ domain binding / cytoplasmic vesicle membrane / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / potassium ion transport / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / postsynaptic membrane / basolateral plasma membrane / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.3 / Tax1-binding protein 3 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / PDZ domain / Pdz3 Domain ...Potassium channel, inwardly rectifying, Kir2.3 / Tax1-binding protein 3 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Immunoglobulin E-set / Roll / Mainly Beta
Similarity search - Domain/homology
Tax1-binding protein 3 / Inward rectifier potassium channel 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShen, Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Molecular mechanism of inward rectifier potassium channel 2.3 regulation by tax-interacting protein-1
Authors: Yan, X. / Zhou, H. / Zhang, J. / Shi, C. / Xie, X. / Wu, Y. / Tian, C. / Shen, Y. / Long, J.
History
DepositionMar 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / 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_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.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_atom_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_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_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: Tax1-binding protein 3
B: Tax1-binding protein 3
C: C-terminal peptide from Inward rectifier potassium channel 4
D: C-terminal peptide from Inward rectifier potassium channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,32812
Polymers29,9244
Non-polymers4038
Water1,910106
1
A: Tax1-binding protein 3
C: C-terminal peptide from Inward rectifier potassium channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0985
Polymers14,9622
Non-polymers1363
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint1 kcal/mol
Surface area6530 Å2
MethodPISA
2
B: Tax1-binding protein 3
D: C-terminal peptide from Inward rectifier potassium channel 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2297
Polymers14,9622
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint0 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.457, 86.457, 101.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Tax1-binding protein 3 / Tax interaction protein 1 / TIP-1 / Glutaminase-interacting protein 3


Mass: 13751.685 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: O14907
#2: Protein/peptide C-terminal peptide from Inward rectifier potassium channel 4 / C-terminal peptide of Inward rectifier K(+) channel Kir2.3


Mass: 1210.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: this sequence occurs naturally in humans / References: UniProt: P48050
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, cacodylate buffer, zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 10830 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 57.4 Å2 / Rsym value: 0.067 / Net I/σ(I): 29.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 873 / Rsym value: 0.371 / % possible all: 81.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DIW

3diw


Resolution: 2.8→29.27 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 83181.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 515 5.3 %RANDOM
Rwork0.247 ---
obs0.247 9632 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7946 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 66 Å2
Baniso -1Baniso -2Baniso -3
1-6.48 Å20 Å20 Å2
2--6.48 Å20 Å2
3----12.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 8 106 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it3.032
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 73 5.1 %
Rwork0.339 1347 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3so4.paramso4.top
X-RAY DIFFRACTION4gol.paramgol.top
X-RAY DIFFRACTION5water_rep.paramwater_rep.top

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