PDB-3g37: Cryo-EM structure of actin filament in the presence of ...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3g37
Title	Cryo-EM structure of actin filament in the presence of phosphate
Descriptor	Actin alpha skeletal muscle
Keywords	CONTRACTILE PROTEIN, actin, cytoskeleton, cell adhesion, cellular signaling, cytokinesis, muscle, cryo-EM, ATP-binding, Methylation, Muscle protein, Nucleotide-binding, Phosphoprotein
Authors	Wakabayshi, T., Murakami, K., Yasunaga, T., Noguchi, T.Q., Uyeda, T.Q.
Date	Deposition: 2009-02-02, Release: 2010-11-03
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-1674, Made by UCSF CHIMERA #3: Superimposing with EM 3D map: EMDB-1674, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1674 CiteFit PDB-3a5l Cite PDB-3a5m Cite PDB-3a5n Cite PDB-3a5o Cite Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3j0s EMDB-1757 PDB-3zys PDB-2wyy List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell, Vol. 143, Issue 2, Page 275-87, Year 2010
Title	Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
Authors	Kenji Murakami, Takuo Yasunaga, Taro Q P Noguchi, Yuki Gomibuchi, Kien X Ngo, Taro Q P Uyeda, Takeyuki Wakabayashi Department of Biosciences, School of Science and Engineering, Teikyo University, Toyosatodai 1-1, Utsunomiya 320-8551, Japan.
Keywords	Actins (chemistry), Adenosine Triphosphate (metabolism, 56-65-5), Animals, Cryoelectron Microscopy, Crystallography, X-Ray, Models, Molecular, Muscle, Skeletal (chemistry), Phosphates (metabolism), Rabbits
Links	PII: S0092-8674(10)01082-2, DOI: 10.1016/j.cell.2010.09.034, PubMed: 20946985

Components
ID 1 : Alpha-actin-1
Image
Description	Actin, alpha skeletal muscle
Type	polymer
Formula weight	41902.020 Da
Number of molecules	12
Source	Method: Isolated from a natural source Common name: rabbit NCBI taxonomy: ID:9986 Organism scientific: Oryctolagus cuniculus Tissue: 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	12
Source	Method: Obtained synthetically
ID 3 : PHOSPHATE ION
Image
Description	PHOSPHATE ION
Type	non-polymer
Formula weight	94.971 Da
Number of molecules	36
Source	Method: Obtained synthetically
ID 4 : MAGNESIUM ION
Image
Description	MAGNESIUM ION
Type	non-polymer
Formula weight	24.305 Da
Number of molecules	72
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	FILAMENT
Details	50 mM NaCl, 5 mM MgCl2, 0.025 mM ATP, 10 mM sodium phosphate (pH 7.4), 0.05 %NaN3, 0.7 mM DTT
Name	actin filament in the presence of phosphate
Buffer
Name	phosphate buffer
Sample preparation
pH	7.4
Vitrification
Cryogen name	ETHANE
Humidity	90
Temp	77 Kelvin

Electron Microscopy
Imaging
Microscope	model: HITACHI EF2000
Electron gun
Electron source	cold Field emission gun
Accelerating voltage	200 kV
Electron dose	15 e/A**2
Illumination mode	SPOT SCAN
Lens
Mode	bright field
Magnification	nominal: 100000 X
Nominal defocus	max: 1500 nm, min: 1000 nm
Energy filter	HITACH
Specimen holder
Specimen holder	model: GATAN LIQUID NITROGEN, type: Side entry liquid nitrogen-cooled cryo specimen holder
Tilt angle	min: 0 degrees, max: 0 degrees
Temperature	77 Kelvin
Recording temperature	maximum: 77, minimum: 77
Detector
Details	CCD camera with an epitaxially-grown CsI scintillator
Type	CCD

Processing
2D projection selection
Software name	O, EOS (Yasunaga & Wakabayshi, 1996)
3D reconstruction
Actual pixel size	2.275 A/pix
CTF correction method	FSC at 0.143 cut-off
Method	single particle
Nominal pixel size	2.275 A/pix
Resolution	6 A
3D fitting
Method	local refinement
Refinement Protocol	real-space refinement
Refinement Space	REAL
Software name	O, EOS (Yasunaga & Wakabayshi, 1996)
Target criteria	pdbRhofit (Yasunaga & Wakabayashi, 1996)
Refine hist
Total atoms	35808
Ligand atoms	576
Protein atoms	35232