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- PDB-6x23: PDZ domain from choanoflagellate SHANK1 (mbSHANK1) bound to GIRK3... -

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Basic information

Entry
Database: PDB / ID: 6x23
TitlePDZ domain from choanoflagellate SHANK1 (mbSHANK1) bound to GIRK3 peptide
Components
  • G protein-activated inward rectifier potassium channel 3
  • mbSHANK1 protein
KeywordsSIGNALING PROTEIN / PDZ / protein-protein interaction / peptide-binding domain / choanoflagellate / Monosiga brevicollis
Function / homology
Function and homology information


synaptic receptor adaptor activity / G-protein activated inward rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / potassium ion import across plasma membrane / ionotropic glutamate receptor binding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.3 / Domain of unknown function DUF3447 / 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 / SAM domain (Sterile alpha motif) / SAM domain profile. ...Potassium channel, inwardly rectifying, Kir3.3 / Domain of unknown function DUF3447 / 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 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin E-set
Similarity search - Domain/homology
Predicted protein / G protein-activated inward rectifier potassium channel 3
Similarity search - Component
Biological speciesMonosiga brevicollis (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsGao, M. / Mackley, I.G.P. / Amacher, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1904711 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis.
Authors: Gao, M. / Mackley, I.G.P. / Mesbahi-Vasey, S. / Bamonte, H.A. / Struyvenberg, S.A. / Landolt, L. / Pederson, N.J. / Williams, L.I. / Bahl, C.D. / Brooks 3rd, L. / Amacher, J.F.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mbSHANK1 protein
B: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)12,4962
Polymers12,4962
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-2 kcal/mol
Surface area5640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.070, 40.690, 78.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mbSHANK1 protein


Mass: 11412.797 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 442-544)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 28170 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9V7E4
#2: Protein/peptide G protein-activated inward rectifier potassium channel 3 / GIRK-3 / Inward rectifier K(+) channel Kir3.3 / Potassium channel / inwardly rectifying subfamily J member 9


Mass: 1083.211 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 384-393) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92806
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.33 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.25 M sodium chloride, 0.1 M Bis-Tris, pH 5.5, 32% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2019
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.15→36.16 Å / Num. obs: 6160 / % possible obs: 99.9 % / Redundancy: 12.57 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.999 / Rsym value: 0.16 / Net I/σ(I): 12.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym value% possible all
2.15-2.5112.682.0322360.8851.5599.7
2.51-2.7513.114.989170.9810.599100

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.154→36.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 189 4.8 %
Rwork0.206 3752 -
obs0.2083 3941 64.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.59 Å2 / Biso mean: 38.0375 Å2 / Biso min: 12.9 Å2
Refinement stepCycle: final / Resolution: 2.154→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms742 0 0 23 765
Biso mean---32.06 -
Num. residues----96
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01753
X-RAY DIFFRACTIONf_angle_d1.3441008
X-RAY DIFFRACTIONf_chiral_restr0.061106
X-RAY DIFFRACTIONf_plane_restr0.007134
X-RAY DIFFRACTIONf_dihedral_angle_d17.747454
LS refinement shellResolution: 2.154→36.16 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2534 189 -
Rwork0.206 3752 -
obs--64 %

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