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Basic information

Entry
Database: PDB / ID: 1m8q
TitleMolecular Models of Averaged Rigor Crossbridges from Tomograms of Insect Flight Muscle
DescriptorChicken Skeletal muscle Myosin II
Rabbit Skeletal muscle Actin
(Chicken Skeletal muscle Myosin II ...) x 2
KeywordsCONTRACTILE PROTEIN / Actin-myosin complex in situ in muscle
Specimen sourceGallus gallus / bird / chicken / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
Oryctolagus cuniculus / mammal / rabbit / アナウサギ /
MethodElectron microscopy (70 Å resolution / Tissue / Tomography)
AuthorsChen, L.F. / Winkler, H. / Reedy, M.K. / Reedy, M.C. / Taylor, K.A.
CitationJ. Struct. Biol., 138, 92-104

primary. J. Struct. Biol., 138, 92-104 Yorodumi Papers
Molecular modeling of averaged rigor crossbridges from tomograms of insect flight muscle.
Li Fan Chen / Hanspeter Winkler / Michael K Reedy / Mary C Reedy / Kenneth A Taylor

#1. J.STRUCT.BIOL., 2001, 133, 221-232
Real space refinement of acto-myosin structures from sectioned muscle.
Chen, L.F. / Blanc, E. / Chapman, M.S. / Taylor, K.A.

#2. ULTRAMICROSCOPY, 1999, 77, 141-152
Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle
Winkler, H. / Taylor, K.A.

#3. J.STRUCT.BIOL., 1997, 120, 372-386
The use of electron tomography for structural analysis of disordered protein arrays.
Taylor, K.A. / Tang, J. / Cheng, Y. / Winkler, H.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 25, 2002 / Release: Sep 10, 2002
RevisionDateData content typeGroupProviderType
1.0Sep 10, 2002Structure modelrepositoryInitial release
1.1Apr 28, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: Skeletal muscle Myosin II
B: Skeletal muscle Myosin II Regulatory Light Chain
C: Skeletal muscle Myosin II Essential Light Chain
D: Skeletal muscle Myosin II
E: Skeletal muscle Myosin II Regulatory Light Chain
F: Skeletal muscle Myosin II Essential Light Chain
G: Skeletal muscle Myosin II
H: Skeletal muscle Myosin II Regulatory Light Chain
I: Skeletal muscle Myosin II Essential Light Chain
P: Skeletal muscle Myosin II
Q: Skeletal muscle Myosin II Regulatory Light Chain
R: Skeletal muscle Myosin II Essential Light Chain
7: Skeletal muscle Actin
8: Skeletal muscle Actin
9: Skeletal muscle Actin
V: Skeletal muscle Actin
W: Skeletal muscle Actin
X: Skeletal muscle Actin
Y: Skeletal muscle Actin
Z: Skeletal muscle Actin
0: Skeletal muscle Actin
1: Skeletal muscle Actin
2: Skeletal muscle Actin
3: Skeletal muscle Actin
4: Skeletal muscle Actin
5: Skeletal muscle Actin


Theoretical massNumber of molelcules
Total (without water)1,101,08626
Polyers1,101,08626
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
Skeletal muscle Myosin II


Mass: 96625.484 Da / Num. of mol.: 4
Source: (natural) Gallus gallus / bird / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
References: UniProt: P13538

Cellular component

Molecular function

#2: Polypeptide(L)
Skeletal muscle Myosin II Regulatory Light Chain


Mass: 16063.036 Da / Num. of mol.: 4
Source: (natural) Gallus gallus / bird / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
References: UniProt: P02609

Cellular component

Molecular function

#3: Polypeptide(L)
Skeletal muscle Myosin II Essential Light Chain


Mass: 16063.926 Da / Num. of mol.: 4
Source: (natural) Gallus gallus / bird / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
References: UniProt: P02604

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)
Skeletal muscle Actin


Mass: 41862.613 Da / Num. of mol.: 14
Source: (natural) Oryctolagus cuniculus / mammal / アナウサギ /
References: UniProt: P68135

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / Reconstruction method: TOMOGRAPHY

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Sample preparation

ComponentName: Insect flight muscle of the large water bug Lethocerus maximus
Type: 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. Models are built to fit the thin, actin containing filaments labeled with endogenous myosin in the rigor state.
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Osmium tetroxide, Uranyl Acetate
VitrificationDetails: No vitrification. Samples were viewed at room temperature.
Crystal grow
*PLUS
Temp unit: K / Method: other / Details: dual axis tilt series electron tomograohy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS EM400
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 17000
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 36
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1RSRefMODEL FITTING
2CustomRECONSTRUCTION
CTF correctionDetails: none
SymmetryPoint symmetry: C1
3D reconstructionMethod: Dual axis tilt series electron tomography / Resolution: 70 Å / Nominal pixel size: 15.5
Magnification calibration: Indicated instrument magnification
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.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--Initial models were fit by hand using O. The fit was then refined using real space refinement. REFINEMENT PROTOCOL--rigid body
Ref protocol: RIGID BODY FIT / Ref space: REAL
Target criteria: Best correlation coefficient and fewest poor contacts
Atomic model building
IDPDB-ID 3D fitting ID
12MYS1
21ATN1
Number of atoms included #LASTProtein: 76872 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 76872

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