PDB-2y83: Actin filament pointed end

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2y83
Title	Actin filament pointed end
Descriptor	ACTIN ALPHA SKELETAL MUSCLE
Keywords	CONTRACTILE PROTEIN, CYTOSKELETON, CELL MOTILITY
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-1872, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1872 Fit PDB-1alm PDB-1atn PDB-1eqy PDB-1esv PDB-1h1v PDB-1ijj PDB-1j6z PDB-1kxp PDB-1lcu PDB-1lot PDB-1m8q PDB-1ma9 PDB-1mvw PDB-1nwk PDB-1o18 PDB-1o19 PDB-1o1a PDB-1o1b PDB-1o1c PDB-1o1d PDB-1o1e PDB-1o1f PDB-1o1g PDB-1p8z PDB-1qz5 PDB-1qz6 PDB-1rdw PDB-1rfq PDB-1rgi PDB-1s22 PDB-1sqk PDB-1t44 PDB-1uy5 PDB-1wua PDB-1y64 PDB-2a3z PDB-2a40 PDB-2a41 PDB-2a42 PDB-2a5x PDB-2asm PDB-2aso PDB-2asp PDB-2d1k PDB-2ff3 PDB-2ff6 PDB-2fxu PDB-2v51 PDB-2v52 PDB-2vcp PDB-2vyp PDB-2w49 PDB-2w4u PDB-4a7f PDB-4a7h PDB-4a7l PDB-4a7n Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-5168 EMDB-1872 PDB-3j0b PDB-3j05 PDB-1nn8 EMDB-1980 List of similar structure data about Omokage system

Article
Citation - primary
Article	Embo J., Vol. 30, Page: 1230 - , Year: 2011,
Title	Structural Basis for the Slow Dynamics of the Actin Filament Pointed End.
Authors	Narita, A., Oda, T., Maeda, Y.
Links	DOI: 10.1038/EMBOJ.2011.48

Components
ID 1 : ALPHA-ACTIN-1
Image
Description	ACTIN, ALPHA SKELETAL MUSCLE
Type	polypeptide(L)
Formula weight	41862.965 Da
Number of molecules	6
ID	1
Source	Method: Isolated from a natural source Common name: RABBIT NCBI taxonomy: ID:9986 Organism scientific: ORYCTOLAGUS CUNICULUS Tissue: SKELETAL MUSCLE
Links	UniProt: P68135, Sequence view
ID 2 : ADENOSINE-5'-DIPHOSPHATE
Image
Description	ADENOSINE-5'-DIPHOSPHATE
Type	non-polymer
Formula weight	427.203 Da
Number of molecules	6
ID	2
Source	Method: Obtained synthetically
ID 3 : CALCIUM ION
Image
Description	CALCIUM ION
Type	non-polymer
Formula weight	40.080 Da
Number of molecules	6
ID	3
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	FILAMENT
Name	RABBIT SKELETAL ACTIN
Buffer
Name	50 MM NACL, 10 MM SODIUM PHOSPHATE BUFFER PH 7.4 3 MM MGCL2, 0.005% (W/V) NAN3, 0.7 MM DTT.
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.4
Sample concentration	0.05 mg/ml
Sample support
Details	HOLEY CARBON
Vitrification
Details	VITRIFICATION 1 - CRYOGEN- ETHANE, HUMIDITY- 90%, TEMPERATURE- 4 DEGREES CELSIUS. METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING.
Experiment
Method	ELECTRON MICROSCOPY

Processing
2D projection selection
Number of particles	714
Software name	EOS
3D reconstruction
Actual pixel size	3.4125 A/pix
CTF correction method	PHASE AND AMPLITUDE
Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1872.
Method	SINGLE PARTICLE ANALYSIS
Nominal pixel size	3.4125 A/pix
Resolution	22.9 A
3D fitting
Method	RIGID BODY AND MOLECULAR DYNAMICS
Refinement Protocol	EM
Refinement Space	REAL
3D fitting list
3D fitting id	1
PDB entry ID	2ZWH PDB-2zwh
Refine
Refine id	ELECTRON MICROSCOPY
Ls d res high	22.90 A
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
D res high	22.90
Total atoms	17766
Ligand atoms	168
Protein atoms	17598