PDB-2xky: SINGLE PARTICLE ANALYSIS OF KIR2.1NC_4 IN NEGATIVE STAIN

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2xky
Title	SINGLE PARTICLE ANALYSIS OF KIR2.1NC_4 IN NEGATIVE STAIN
Descriptor	INWARD RECTIFIER POTASSIUM CHANNEL 2
Keywords	METAL TRANSPORT, ION CHANNEL, MEMBRANE PROTEIN
Authors	Fomina, S., Howard, T.D., Sleator, O.K., Golovanova, M., O'Ryan, L., Leyland, M.L., Grossmann, J.G., Collins, R.F., Prince, S.M.
Date	Deposition: 2010-07-15, Release: 2011-07-20
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with EM 3D map: EMDB-1764, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1764 CiteFit EMDB-1761 Cite EMDB-1765 Cite EMDB-1766 Cite PDB-2xkx Cite PDB-1u4f PDB-2gix Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3deg PDB-3j2k PDB-1m11 EMDB-2189 List of similar structure data about Omokage system

Article
Citation - primary
Article	Biochim. Biophys. Acta, Vol. 1808, Issue 10, Page 2374-89, Year 2011
Title	Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95.
Authors	Svetlana 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.
Keywords	Cytoplasm (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
Links	DOI: 10.1016/j.bbamem.2011.06.021, PubMed: 21756874
Citation - 1
Article	Nat. Neurosci., Vol. 8, Issue 3, Page 279-87, Year 2005
Title	Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification.
Authors	Scott Pegan, Christine Arrabit, Wei Zhou, Witek Kwiatkowski, Anthony Collins, Paul A Slesinger, Senyon Choe Structural Biology, The Salk Institute, La Jolla, California 92037, USA.
Keywords	Amino 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, 7440-09-7), Potassium Channels, Inwardly Rectifying (chemistry), Protein Conformation, Protein Structure, Tertiary (physiology), Recombinant Fusion Proteins (chemistry), Xenopus laevis
Links	DOI: 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
Description	INWARD RECTIFIER POTASSIUM CHANNEL 2
Type	polymer
Fragment	KIR2.1 CYTOPLASMIC DOMAIN, RESIDUES 1-67,189-428
Formula weight	34980.535 Da
Number of molecules	4
Details	HOMOTETRAMER OF FUSED N, C TERMINI
Source	Method: Isolated from a genetically manipulated source Gene: MOUSE, ID:10090, MUS MUSCULUS Host: ID:511693, ESCHERICHIA COLI , BL21, PLASMID Plasmid name: PET15B
Links	UniProt: P35561, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	MOUSE KIR2.1, CYTOPLASMIC DOMAIN
Buffer
Name	20MM TRIS/HCL, 150MM NACL, 1MM REDUCED GSH, 1MM EDTA, 50MM L-GLUTAMIC ACID, 50MM L-ARGININE
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	NEGATIVE STAIN
Sample preparation
pH	7.5
Sample concentration	1.0 mg/ml
Sample support
Details	CARBON

Electron Microscopy
Imaging
Microscope	model: OTHER
Details	LOW DOSE
Electron gun
Electron source	TUNGSTEN HAIRPIN
Accelerating voltage	100 kV
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Cs	nominal: 2.0 mm
Nominal defocus	max: 1250 nm, min: 600 nm
Specimen holder
Tilt angle	min: 0 degrees, max: 0.1 degrees
Detector
Type	GATAN ORIUS CCD CAMERA
Image scans
Number digital images	22

Processing
2D projection selection
Number of particles	49012
Software name	EMAN
3D reconstruction
Actual pixel size	2.93 A/pix
CTF correction method	PARAMETERS DETERMINED USING SCATTERING CURVE
Details	THE 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 size	2.93 A/pix
Resolution	17.2 A
3D fitting
Method	A 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 Protocol	DOCKED USING CHIMERA
Refinement Space	REAL
Refine
Ls d res high	17.20 A
ID	1
Refine hist
D res high	17.20
Total atoms	1236
Protein atoms	1236