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

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Entry
Database: PDB / ID: 3qdo
TitleCrystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused to the Gly-Gly linker followed by C-terminal (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


postsynaptic early endosome / G-protein activated inward rectifier potassium channel activity / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / regulation of presynaptic membrane potential / neurotransmitter receptor transport to plasma membrane / postsynaptic recycling endosome / WASH complex / response to methamphetamine hydrochloride / retromer complex ...postsynaptic early endosome / G-protein activated inward rectifier potassium channel activity / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / regulation of presynaptic membrane potential / neurotransmitter receptor transport to plasma membrane / postsynaptic recycling endosome / WASH complex / response to methamphetamine hydrochloride / retromer complex / endosome to plasma membrane protein transport / regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / regulation of synapse maturation / phosphatidylinositol-3-phosphate binding / endocytic recycling / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / endosomal transport / endosome to lysosome transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / immunological synapse / monoatomic ion channel complex / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / phosphatidylinositol binding / PDZ domain binding / intracellular protein transport / cellular response to nerve growth factor stimulus / Schaffer collateral - CA1 synapse / calcium-dependent protein binding / nervous system development / presynaptic membrane / early endosome membrane / early endosome / postsynapse / 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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / PhoX homologous domain, present in p47phox and p40phox. ...Potassium channel, inwardly rectifying, Kir3.3 / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / 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 / Roll / Ubiquitin-like domain superfamily / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 18, 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)11,3451
Polymers11,3451
Non-polymers00
Water1,946108
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)22,6902
Polymers22,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area2340 Å2
ΔGint-6 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.795, 59.795, 53.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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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: 11344.750 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 / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4V4, UniProt: Q63511
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A IS A CHIMERA: SNX27 PDZ DOMAIN (UNP RESIDUES 39-133), ENGINEERED LINKER, GIRK-3 C-TERMINUS ...CHAIN A IS A CHIMERA: SNX27 PDZ DOMAIN (UNP RESIDUES 39-133), ENGINEERED LINKER, 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: 2.11 Å3/Da / Density % sol: 41.76 %
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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 27, 2009 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→42.28 Å / Num. all: 7380 / Num. obs: 7380 / % possible obs: 99.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 14.216 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.3
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 19.4 / Num. unique all: 384 / % possible all: 100

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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 3QE1

3qe1


Resolution: 1.88→42.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.514 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20305 354 4.6 %RANDOM
Rwork0.14427 ---
obs0.14688 7380 99.79 %-
all-7380 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.88→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 0 108 906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021806
X-RAY DIFFRACTIONr_angle_refined_deg2.021.9731085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06323.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26915139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.101158
X-RAY DIFFRACTIONr_chiral_restr0.2230.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021609
X-RAY DIFFRACTIONr_mcbond_it1.4051.5530
X-RAY DIFFRACTIONr_mcangle_it2.4322842
X-RAY DIFFRACTIONr_scbond_it3.3923276
X-RAY DIFFRACTIONr_scangle_it5.724.5243
LS refinement shellResolution: 1.881→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 22 -
Rwork0.147 567 -
obs-589 100 %

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