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Single particle analysis of Kir2.1NC_4 in negative stain

by single particle reconstruction, at 17.2 A resolution

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#2: Superimposing with EM 3D map: EMDB-1764, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2xky
TitleSingle particle analysis of Kir2.1NC_4 in negative stain
DescriptorINWARD RECTIFIER POTASSIUM CHANNEL 2
KeywordsMETAL TRANSPORT, ION CHANNEL, MEMBRANE PROTEIN
AuthorsFomina, S., Howard, T.D., Sleator, O.K., Golovanova, M., O'Ryan, L., Leyland, M.L., Grossmann, J.G., Collins, R.F., Prince, S.M.
DateDeposition: 2010-07-15, Release: 2011-07-20
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
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#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-1764, Made by UCSF CHIMERA

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EMDB-1764

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Article
Citation - primary
ArticleBiochim. Biophys. Acta, Vol. 1808, Issue 10, Page 2374-89, Year 2011
TitleSelf-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95.
AuthorsSvetlana Fomina, Tina D Howard, Olivia K Sleator, Marina Golovanova, Liam O'Ryan, Mark L Leyland, J Günter Grossmann, Richard F Collins, Stephen M Prince
University of Manchester, Manchester Interdisciplinary Biocentre, Manchester M1 7DN, UK.
KeywordsCytoplasm (metabolism), DLG4 protein, human, Humans, Intracellular Signaling Peptides and Proteins (chemistry), Kir2.1 channel, Membrane Proteins (chemistry), Microscopy, Electron, Transmission, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Potassium Channels, Inwardly Rectifying (chemistry), Protein Binding, Reproducibility of Results, Scattering, Radiation
LinksDOI: 10.1016/j.bbamem.2011.06.021, PubMed: 21756874
Citation - 1
ArticleNat. Neurosci., Vol. 8, Issue 3, Page 279-87, Year 2005
TitleCytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification.
AuthorsScott Pegan, Christine Arrabit, Wei Zhou, Witek Kwiatkowski, Anthony Collins, Paul A Slesinger, Senyon Choe
Structural Biology, The Salk Institute, La Jolla, California 92037, USA.
KeywordsAmino Acid Sequence, Analysis of Variance, Animals, Cloning, Molecular (methods), Crystallography (methods), Dose-Response Relationship, Drug, Electric Conductivity, G Protein-Coupled Inwardly-Rectifying Potassium Channels, GTP-Binding Protein beta Subunits (genetics), Ion Channel Gating (drug effects), Kir2.1 channel, Macromolecular Substances, Membrane Potentials (drug effects), Molecular Sequence Data, Mutagenesis, Site-Directed (physiology), Patch-Clamp Techniques (methods), Phosphatidylinositol 4,5-Diphosphate (metabolism), Potassium (pharmacology), Potassium Channels, Inwardly Rectifying (chemistry), Protein Conformation, Protein Structure, Tertiary (physiology), Recombinant Fusion Proteins (chemistry), Xenopus laevis
LinksDOI: 10.1038/nn1411, PubMed: 15723059
Components
ID 1 : POTASSIUM CHANNEL, INWARDLY RECTIFYING SUBFAMILY J MEMBER 2, INWARD RECTIFIER K(+) CHANNEL KIR2.1, IRK-1
Image
DescriptionINWARD RECTIFIER POTASSIUM CHANNEL 2
Typepolypeptide(L)
FragmentKIR2.1 CYTOPLASMIC DOMAIN, RESIDUES 1-67,189-428
Formula weight34980.535 Da
Number of molecules4
ID1
DetailsHOMOTETRAMER OF FUSED N, C TERMINI
SourceMethod: Isolated from a genetically manipulated source
Gene: MOUSE, ID:10090, MUS MUSCULUS
Host: ID:511693, ESCHERICHIA COLI

, BL21, PLASMID
Plasmid name: PET15B
LinksUniProt: P35561, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameMOUSE KIR2.1, CYTOPLASMIC DOMAIN
Buffer
Name20MM TRIS/HCL, 150MM NACL, 1MM REDUCED GSH, 1MM EDTA, 50MM L-GLUTAMIC ACID, 50MM L-ARGININE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeNEGATIVE STAIN
Sample preparation
pH7.5
Sample concentration1.0 mg/ml
Sample support
DetailsCARBON
Experiment
MethodELECTRON MICROSCOPY
Experiment
MethodSOLUTION SCATTERING
Electron Microscopy
Imaging
MicroscopeModel: OTHER
DetailsLOW DOSE
Electron gun
Electron sourceTUNGSTEN HAIRPIN
Accelerating voltage100 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
CsNominal: 2.0 mm
Nominal defocusMax: 1250 nm, Min: 600 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0.1 degrees
Detector
TypeGATAN ORIUS CCD CAMERA
Image scans
Number digital images22
Processing
2D projection selection
Number of particles49012
Software nameEMAN
3D reconstruction
Actual pixel size2.93 A/pix
CTF correction methodPARAMETERS DETERMINED USING SCATTERING CURVE
DetailsTHE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, THIS COMPOSITE STRUCTURE IS THEN FITTED INTO AN EM MAP. MODEL GENERATED FROM SAXS REFINEMENT USING BUNCH. PETOUKHOV, M. V. AND SVERGUN, D. I. (2005). BIOPHYS J 89, 1237-50. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1764. (DEPOSITION ID: 7401).
Nominal pixel size2.93 A/pix
Resolution17.2 A
3D fitting
MethodA MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE EXPERIMENTAL MAP BY MAXIMIZING THE CROSS-CORRELATION WITH THE EXPERIMENTAL MAP. THE COORDINATES WERE THEN REPLACED IN THE CALCULATED MAP TO GENERATE THE FINAL ENTRY.
Refinement ProtocolDOCKED USING CHIMERA
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID1U4F
Refine
Refine idELECTRON MICROSCOPY
Ls d res high17.20 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high17.20
Total atoms1236
Protein atoms1236
Download
PDB format
Allpdb2xky.ent.gz
pdb2xky.ent (uncompressed file)
Header onlypdb2xky.ent.gz
mmCIF format
mmCIF2xky.cif.gz
XML format
All2xky.xml.gz
No-atom2xky-noatom.xml.gz
Ext-atom2xky-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.1 MB