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- PDB-3qgl: Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) in co... -

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Basic information

Entry
Database: PDB / ID: 3qgl
TitleCrystal Structure of PDZ domain of sorting nexin 27 (SNX27) in complex with the ESESKV peptide corresponding to the C-terminal tail of GIRK3
Components
  • G protein-activated inward rectifier potassium channel 3
  • Sorting nexin-27
KeywordsPROTEIN BINDING / PDZ domain / PDZ binding / GIRK3 regulation / early endosomes / brain / neurons
Function / homology
Function and homology information


postsynaptic early endosome / establishment of protein localization to plasma membrane / G-protein activated inward rectifier potassium channel activity / positive regulation of AMPA glutamate receptor clustering / regulation of presynaptic membrane potential / response to methamphetamine hydrochloride / neurotransmitter receptor transport to plasma membrane / WASH complex / postsynaptic recycling endosome / retromer complex ...postsynaptic early endosome / establishment of protein localization to plasma membrane / G-protein activated inward rectifier potassium channel activity / positive regulation of AMPA glutamate receptor clustering / regulation of presynaptic membrane potential / response to methamphetamine hydrochloride / neurotransmitter receptor transport to plasma membrane / WASH complex / postsynaptic recycling endosome / retromer complex / endosome to plasma membrane protein transport / inward rectifier potassium channel activity / regulation of synapse maturation / regulation of monoatomic ion transmembrane transport / endocytic recycling / phosphatidylinositol-3-phosphate binding / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-27
F: G protein-activated inward rectifier potassium channel 3
B: Sorting nexin-27
G: G protein-activated inward rectifier potassium channel 3
C: Sorting nexin-27
H: G protein-activated inward rectifier potassium channel 3
D: Sorting nexin-27
I: G protein-activated inward rectifier potassium channel 3
E: Sorting nexin-27
J: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)56,24310
Polymers56,24310
Non-polymers00
Water905
1
A: Sorting nexin-27
F: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-2 kcal/mol
Surface area5630 Å2
MethodPISA
2
B: Sorting nexin-27
G: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-2 kcal/mol
Surface area5660 Å2
MethodPISA
3
C: Sorting nexin-27
H: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2 kcal/mol
Surface area5640 Å2
MethodPISA
4
D: Sorting nexin-27
I: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2 kcal/mol
Surface area5650 Å2
MethodPISA
5
E: Sorting nexin-27
J: G protein-activated inward rectifier potassium channel 3


Theoretical massNumber of molelcules
Total (without water)11,2492
Polymers11,2492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-2 kcal/mol
Surface area5670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.571, 81.567, 90.678
Angle α, β, γ (deg.)90.00, 102.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12F
22G
32H
42I
52J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A38 - 133
2111B38 - 133
3111C38 - 133
4111D38 - 133
5111E38 - 133
1125F201 - 206
2125G201 - 206
3125H201 - 206
4125I201 - 206
5125J201 - 206

NCS ensembles :
ID
1
2

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Components

#1: Protein
Sorting nexin-27 / SNX27 / MAP-responsive gene protein / Methamphetamine-responsive transcript 1 protein / PDZ-protein Mrt1


Mass: 10569.952 Da / Num. of mol.: 5 / Fragment: PDZ domain (UNP residues 39-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mrt1, Snx27 / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4V4
#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: 678.709 Da / Num. of mol.: 5 / Fragment: C-terminus (UNP residues 388-393) / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q63511
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0 M sodium formate, pH 7.0, 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: 3.3→38.949 Å / Num. all: 9810 / Num. obs: 9810 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 90.692 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.72
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 6.08 / Num. unique all: 475 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QE1

3qe1


Resolution: 3.31→38.949 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.848 / SU B: 58.041 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25434 470 4.8 %RANDOM
Rwork0.23365 ---
obs0.23462 9329 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-2.61 Å2
2--5.43 Å20 Å2
3----7.37 Å2
Refinement stepCycle: LAST / Resolution: 3.31→38.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 0 5 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223845
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9835180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5285500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26623.636165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65615685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9851540
X-RAY DIFFRACTIONr_chiral_restr0.0770.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212875
X-RAY DIFFRACTIONr_mcbond_it01.52500
X-RAY DIFFRACTIONr_mcangle_it024000
X-RAY DIFFRACTIONr_scbond_it031345
X-RAY DIFFRACTIONr_scangle_it04.51180
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A716tight positional0.020.05
11B716tight positional0.030.05
11C716tight positional0.020.05
11D716tight positional0.030.05
11E716tight positional0.020.05
22A24medium positional0.10.5
22B24medium positional0.070.5
22C24medium positional0.070.5
22D24medium positional0.080.5
22E24medium positional0.120.5
22A23loose positional0.25
22B23loose positional0.25
22C23loose positional0.25
22D23loose positional0.325
22E23loose positional0.385
11A716tight thermal00.5
11B716tight thermal00.5
11C716tight thermal00.5
11D716tight thermal00.5
11E716tight thermal00.5
22A24medium thermal02
22B24medium thermal02
22C24medium thermal02
22D24medium thermal02
22E24medium thermal02
22A23loose thermal010
22B23loose thermal010
22C23loose thermal010
22D23loose thermal010
22E23loose thermal010
LS refinement shellResolution: 3.305→3.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 31 -
Rwork0.254 658 -
obs-689 93.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.852-0.8423-2.14637.54891.24896.954-0.1493-0.1191-0.12210.340.1234-0.35720.3507-0.16380.02590.234-0.0165-0.0380.2648-0.02180.50923.9098.36320.578
28.0675-0.4322-0.89138.07770.3196.33-0.26320.1835-0.0601-0.1050.19360.14840.4623-0.0150.06960.20780.03280.01390.21070.06040.44244.3214.8377.347
37.77421.29190.35277.18420.398210.80190.2307-0.12450.23130.292-0.2329-0.00410.447-0.47790.00220.5199-0.01640.0140.28260.04140.43294.118-11.9928.803
411.67061.89223.42248.97632.800613.3363-0.33240.4072-0.07050.42460.3146-0.85090.33291.20490.01780.49030.0341-0.07990.3467-0.09560.58589.342-24.068.485
56.1290.3142-1.57458.14640.89799.4136-0.00610.34190.28480.11350.2291-0.56480.23121.6237-0.2230.55750.0569-0.03580.7828-0.19620.670930.70623.01538.125
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 133
2X-RAY DIFFRACTION1F201 - 206
3X-RAY DIFFRACTION2B39 - 133
4X-RAY DIFFRACTION2G201 - 206
5X-RAY DIFFRACTION3C39 - 133
6X-RAY DIFFRACTION3H201 - 206
7X-RAY DIFFRACTION4D39 - 133
8X-RAY DIFFRACTION4I201 - 206
9X-RAY DIFFRACTION5E39 - 133
10X-RAY DIFFRACTION5J201 - 206

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