PDB-1m8q: Molecular Models of Averaged Rigor Crossbridges from To...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1m8q
Title	Molecular Models of Averaged Rigor Crossbridges from Tomograms of Insect Flight Muscle
Descriptor	Chicken Skeletal muscle Myosin II Chicken Skeletal muscle Myosin II Regulatory Light Chain Chicken Skeletal muscle Myosin II Essential Light Chain Rabbit Skeletal muscle Actin
Keywords	CONTRACTILE PROTEIN, Actin-myosin complex in situ in muscle
Authors	Chen, L.F., Winkler, H., Reedy, M.K., Reedy, M.C., Taylor, K.A.
Date	Deposition: 2002-07-25, Release: 2002-09-10
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
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1001 Fit PDB-1mvw Cite PDB-1o18 Cite PDB-1o19 Cite PDB-1o1a Cite PDB-1o1b Cite PDB-1o1c Cite PDB-1o1d Cite PDB-1o1e Cite PDB-1o1f Cite PDB-1o1g Cite PDB-1atn PDB-2mys PDB-2w49 PDB-2w4a PDB-2w4g PDB-2w4h PDB-2w4u PDB-2y83 PDB-4a7f PDB-4a7h PDB-4a7l PDB-4a7n Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-1o1c PDB-1o19 PDB-1o1b PDB-1o1d List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Struct. Biol., Vol. 138, Issue 1-2, Page 92-104
Title	Molecular modeling of averaged rigor crossbridges from tomograms of insect flight muscle.
Authors	Li Fan Chen, Hanspeter Winkler, Michael K Reedy, Mary C Reedy, Kenneth A Taylor Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.
Keywords	Actomyosin (chemistry, 9013-26-7), Animals, Flight, Animal, Hemiptera, Insects, Microscopy, Electron, Models, Molecular, Muscle Fibers, Skeletal (chemistry), Muscle Proteins (chemistry), Muscle, Skeletal (chemistry), Tomography, X-Ray Computed
Links	PubMed: 12160705, PII: S1047847702000138
Citation - 1
Article	J.STRUCT.BIOL., Vol. 133, Page: 221 - 232, Year: 2001,
Title	Real space refinement of acto-myosin structures from sectioned muscle.
Authors	Chen, L.F., Blanc, E., Chapman, M.S., Taylor, K.A.
Links	DOI: 10.1006/jsbi.2000.4321
Citation - 2
Article	ULTRAMICROSCOPY, Vol. 77, Page: 141 - 152, Year: 1999,
Title	Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle
Authors	Winkler, H., Taylor, K.A.
Links	DOI: 10.1016/S0304-3991(99)00035-2
Citation - 3
Article	J.STRUCT.BIOL., Vol. 120, Page: 372 - 386, Year: 1997,
Title	The use of electron tomography for structural analysis of disordered protein arrays.
Authors	Taylor, K.A., Tang, J., Cheng, Y., Winkler, H.
Links	DOI: 10.1006/jsbi.1997.3932

Components
ID 1 : Skeletal muscle Myosin II
Image
Description	Skeletal muscle Myosin II
Type	polymer
Formula weight	96626.203 Da
Number of molecules	4
Source	Method: Isolated from a natural source Common name: chicken Details: Organism from which the myosin for the crystal structure that provided 2MYS was obtained Genus: Gallus NCBI taxonomy: ID:9031 Organism scientific: Gallus gallus
Links	UniProt: P13538, Sequence view
ID 2 : Skeletal muscle Myosin II Regulatory Light Chain
Image
Description	Skeletal muscle Myosin II Regulatory Light Chain
Type	polymer
Formula weight	16063.167 Da
Number of molecules	4
Source	Method: Isolated from a natural source Common name: chicken Details: Organism from which the myosin for the crystal structure that provided 2MYS was obtained Genus: Gallus NCBI taxonomy: ID:9031 Organism scientific: Gallus gallus
Links	UniProt: P02609, Sequence view
ID 3 : Skeletal muscle Myosin II Essential Light Chain
Image
Description	Skeletal muscle Myosin II Essential Light Chain
Type	polymer
Formula weight	16064.055 Da
Number of molecules	4
Source	Method: Isolated from a natural source Common name: chicken Details: Organism from which the Myosin for the crystal structure that provided 2MYS was obtained Genus: Gallus NCBI taxonomy: ID:9031 Organism scientific: Gallus gallus
Links	UniProt: P02604, Sequence view
ID 4 : Skeletal muscle Actin
Image
Description	Skeletal muscle Actin
Type	polymer
Formula weight	41862.965 Da
Number of molecules	14
Source	Method: Isolated from a natural source Common name: rabbit Details: Organism from which the Actin that provided the crystal structure for 1ATN was obtained Genus: Oryctolagus NCBI taxonomy: ID:9986 Organism scientific: Oryctolagus cuniculus
Links	UniProt: P68135, Sequence view

Sample
Assembly
Aggregation state	TISSUE
Details	Dorsal longitudinal flight muscles of the large waterbug, Lethocerus maximus were glycerinated in the dissected thorax and stored at -20 degrees C. Fixation involved sequential tannic acid-glutaraldehyde (0.2% and 2%), cold 1% OsO4 at pH 6.0, 1% uranyl acetate block staining and Araldite 506 emgedding. Thin sections were stained with a sequence of permanganate and lead. Section were ~25 nm thick.
Name	Insect flight muscle
Entity assembly
Details	Models are built to fit the thin, actin containing filaments labeled with endogenous myosin in the rigor state
Name	Insect flight muscle of the large water bug Lethocerus maximus
Experiment
Reconstruction method	TOMOGRAPHY
Specimen type	FREEZE SUBSTITUTION
Vitrification
Details	No vitrification. Samples were viewed at room temperature.

Electron Microscopy
Detector
Type	Kodak S0163 Film
Image scans
Number digital images	36

Processing
2D projection selection
Software name	RSref
3D reconstruction
CTF correction method	none
Details	3-D motifs were identified in the tomogram by first producing a cross correlation map from which peak coordinates were determined from their center of gravity. We define a 3-D motif as one, entire 38.7 nm crossbridge repeat along actin. These motifs usually contain at least four myosin heads in two paired crossbridges (single chevrons) and sometimes contain as many as six myosin heads in four paired crossbridges (double chevrons). The reference for the analysis was selected to be centered between successive troponin densities which could be identified from the in-plane projection. The individual crossbridge motifs were then subjected to multivariate statistical analysis to identify clusters of motifs showing similar crossbridge structure. These clusters formed the class averages. The choice of structure to be classified was decided by the resolution and the later process of model building. Averaging was done according to the heirarchical ascendent method. The resolution in each of the class averages was 7 nm by the spectral signal to noise ratio.
Magnification calibration	Indicated instrument magnification
Method	Dual axis tilt series electron tomography
Nominal pixel size	15.5 A/pix
Resolution	70 A
3D fitting
Method	Initial models were fit by hand using "O". The fit was then refined using real space refinement.
Refinement Protocol	rigid body
Refinement Space	REAL
Software name	RSref
Target criteria	Best correlation coefficient and fewest poor contacts
Refine hist
Total atoms	76872
Protein atoms	76872