[English] 日本語
Yorodumi
- PDB-3qe1: Crystal Structure of PDZ domain of sorting nexin 27 (SNX27) fused... -

+
Open data


ID or keywords:

Loading...

-
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


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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more