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- PDB-3qe1: Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused... -

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Basic information

Entry
Database: PDB / ID: 3qe1
TitleCrystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused to the C-terminal residues (ESESKV) of GIRK3
ComponentsSorting nexin-27, G protein-activated inward rectifier potassium channel 3 chimera
KeywordsPROTEIN BINDING / PDZ domain / PDZ binding / GIRK3 regulation / early endosomes / brain / neurons
Function / homology
Function and homology information


response to methamphetamine hydrochloride / regulation of presynaptic membrane potential / G-protein activated inward rectifier potassium channel activity / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / retromer complex / inward rectifier potassium channel activity / Activation of G protein gated Potassium channels ...response to methamphetamine hydrochloride / regulation of presynaptic membrane potential / G-protein activated inward rectifier potassium channel activity / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / retromer complex / inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / phosphatidylinositol-3-phosphate binding / endocytic recycling / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / endosomal transport / monoatomic ion channel complex / potassium ion import across plasma membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / ionotropic glutamate receptor binding / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / PDZ domain binding / intracellular protein transport / Schaffer collateral - CA1 synapse / presynaptic membrane / nervous system development / early endosome membrane / early endosome / endosome / glutamatergic synapse / signal transduction / plasma membrane / cytosol
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.3 / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain ...Potassium channel, inwardly rectifying, Kir3.3 / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 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 / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
G protein-activated inward rectifier potassium channel 3 / Sorting nexin-27
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBalana, B. / Kwiatkowski, W. / Choe, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Mechanism underlying selective regulation of G protein-gated inwardly rectifying potassium channels by the psychostimulant-sensitive sorting nexin 27.
Authors: Balana, B. / Maslennikov, I. / Kwiatkowski, W. / Stern, K.M. / Bahima, L. / Choe, S. / Slesinger, P.A.
History
DepositionJan 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Sorting nexin-27, G protein-activated inward rectifier potassium channel 3 chimera


Theoretical massNumber of molelcules
Total (without water)11,2311
Polymers11,2311
Non-polymers00
Water2,162120
1
A: Sorting nexin-27, G protein-activated inward rectifier potassium channel 3 chimera

A: Sorting nexin-27, G protein-activated inward rectifier potassium channel 3 chimera


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,4612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-y+2/3,x-y+1/3,z+1/31
Unit cell
Length a, b, c (Å)75.789, 75.789, 40.939
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Sorting nexin-27, G protein-activated inward rectifier potassium channel 3 chimera / / SNX27 / MAP-responsive gene protein / Methamphetamine-responsive transcript 1 protein / PDZ-protein ...SNX27 / MAP-responsive gene protein / Methamphetamine-responsive transcript 1 protein / PDZ-protein Mrt1 / GIRK-3 / Inward rectifier K(+) channel Kir3.3 / Potassium channel / inwardly rectifying subfamily J member 9


Mass: 11230.646 Da / Num. of mol.: 1
Fragment: PDZ domain (UNP residues 39-133), GIRK-3 C-terminus (UNP residues 388-393)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mrt1, Kcnj9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4V4, UniProt: Q63511
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A IS A CHIMERA: SNX27 PDZ DOMAIN (UNP RESIDUES 39-133), GIRK-3 C-TERMINUS (UNP RESIDUES 388-393)

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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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES, 28% v/v PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 26, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 8921 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 39.25 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 39.53
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.68 / Num. unique all: 232 / % possible all: 45.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OCS

2ocs


Resolution: 1.68→37.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.178 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22276 417 4.7 %RANDOM
Rwork0.15804 ---
obs0.1609 8503 89.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.419 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.68→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 0 120 882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022769
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9791037
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9423.63633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05415137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.174158
X-RAY DIFFRACTIONr_chiral_restr0.1270.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021575
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3371.5500
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3192801
X-RAY DIFFRACTIONr_scbond_it3.4663269
X-RAY DIFFRACTIONr_scangle_it5.8984.5236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 16 -
Rwork0.264 352 -
obs-368 48.04 %

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