+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1001 | |||||||||
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Title | Real space refinement of acto-myosin structures from sectioned muscle. | |||||||||
Map data | Acto-myosin structures from sectioned muscle | |||||||||
Sample |
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Function / homology | Function and homology information regulation of myosin II filament assembly / contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin II complex / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / myofibril / tropomyosin binding ...regulation of myosin II filament assembly / contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin II complex / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / myofibril / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / muscle contraction / stress fiber / skeletal muscle tissue development / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / calcium-dependent protein binding / lamellipodium / cell body / calmodulin binding / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Lethocerus (insect) | |||||||||
Method | electron tomography / negative staining / Resolution: 40.0 Å | |||||||||
Authors | Chen LF / Blanc E / Chapman MS / Taylor KA | |||||||||
Citation | Journal: J Struct Biol / Year: 2001 Title: Real space refinement of acto-myosin structures from sectioned muscle. Authors: L F Chen / E Blanc / M S Chapman / K A Taylor / Abstract: We have adapted a real space refinement protocol originally developed for high-resolution crystallographic analysis for use in fitting atomic models of actin filaments and myosin subfragment 1 (S1) ...We have adapted a real space refinement protocol originally developed for high-resolution crystallographic analysis for use in fitting atomic models of actin filaments and myosin subfragment 1 (S1) to 3-D images of thin-sectioned, plastic-embedded whole muscle. The rationale for this effort is to obtain a refinement protocol that will optimize the fit of the model to the density obtained by electron microscopy and correct for poor geometry introduced during the manual fitting of a high-resolution atomic model into a lower resolution 3-D image. The starting atomic model consisted of a rigor acto-S1 model obtained by X-ray crystallography and helical reconstruction of electron micrographs. This model was rebuilt to fit 3-D images of rigor insect flight muscle at a resolution of 7 nm obtained by electron tomography and image averaging. Our highly constrained real space refinement resulted in modest improvements in the agreement of model and reconstruction but reduced the number of conflicting atomic contacts by 70% without loss of fit to the 3-D density. The methodology seems to be well suited to the derivation of stereochemically reasonable atomic models that are consistent with experimentally determined 3-D reconstructions computed from electron micrographs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1001.map.gz | 38 MB | EMDB map data format | |
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Header (meta data) | emd-1001-v30.xml emd-1001.xml | 70.2 KB 70.2 KB | Display Display | EMDB header |
Images | 1001.gif | 60.3 KB | ||
Masks | emd_1001_msk_1.map emd_1001_msk_10.map emd_1001_msk_11.map emd_1001_msk_12.map emd_1001_msk_13.map emd_1001_msk_14.map emd_1001_msk_15.map emd_1001_msk_16.map emd_1001_msk_17.map emd_1001_msk_18.map emd_1001_msk_19.map emd_1001_msk_2.map emd_1001_msk_20.map emd_1001_msk_21.map emd_1001_msk_22.map emd_1001_msk_23.map emd_1001_msk_24.map emd_1001_msk_25.map emd_1001_msk_26.map emd_1001_msk_3.map emd_1001_msk_4.map emd_1001_msk_5.map emd_1001_msk_6.map emd_1001_msk_7.map emd_1001_msk_8.map emd_1001_msk_9.map | 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 34.8 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB 136 KB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1001 | HTTPS FTP |
-Validation report
Summary document | emd_1001_validation.pdf.gz | 274.1 KB | Display | EMDB validaton report |
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Full document | emd_1001_full_validation.pdf.gz | 273.7 KB | Display | |
Data in XML | emd_1001_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1001 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1001 | HTTPS FTP |
-Related structure data
Related structure data | 1m8qMK 1mvwMK 1o18MK 1o19MK 1o1aMK 1o1bMK 1o1cMK 1o1dMK 1o1eMK 1o1fMK 1o1gMK M: atomic model generated by this map K: fitted to "mask" map*YM |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1001.map.gz / Format: CCP4 / Size: 40.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Acto-myosin structures from sectioned muscle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 15.4667 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Segmentation: #2
+Segmentation: #11
+Segmentation: #12
+Segmentation: #13
+Segmentation: #14
+Segmentation: #15
+Segmentation: #16
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+Segmentation: #26
+Segmentation: #1
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+Segmentation: #10
-Sample components
-Entire : Rigor insect flight muscle from Lethocerus maximus
Entire | Name: Rigor insect flight muscle from Lethocerus maximus |
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Components |
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-Supramolecule #1000: Rigor insect flight muscle from Lethocerus maximus
Supramolecule | Name: Rigor insect flight muscle from Lethocerus maximus / type: sample / ID: 1000 Details: The sample is a single filament layer cut from myofibrils by ultramicrotomy. The section thickness is ~25 nm. Specimen has been chemically fixed, dehydrated, embedded in Araldite and ...Details: The sample is a single filament layer cut from myofibrils by ultramicrotomy. The section thickness is ~25 nm. Specimen has been chemically fixed, dehydrated, embedded in Araldite and sectioned with a diamond knife. Oligomeric state: Thick myosin containing filament and thin actin-containing filaments. Number unique components: 2 |
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-Supramolecule #1: thick, myosin-containing filament
Supramolecule | Name: thick, myosin-containing filament / type: organelle_or_cellular_component / ID: 1 / Name.synonym: myosin / Details: Filaments contain more than just myosin / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Lethocerus (insect) / synonym: water bug, Lethocerus maximus / Tissue: Indirect flight muscles / Cell: muscle fibers / Organelle: myofibrils / Location in cell: myofibrils |
-Supramolecule #2: thin, actin-containing filament
Supramolecule | Name: thin, actin-containing filament / type: organelle_or_cellular_component / ID: 2 / Name.synonym: actin / Details: filaments contain more than just actin Oligomeric state: polar, 2-stranded helical filament, helical symmetry is 28/13 Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Lethocerus (insect) / synonym: water bug, Lethocerus maximus / Tissue: Indirect flight muscles / Cell: Muscle fibers / Organelle: myofibrils / Location in cell: myofibrils |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | electron tomography |
-Sample preparation
Vitrification | Cryogen name: NONE |
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-Electron microscopy
Microscope | FEI/PHILIPS EM400 |
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Temperature | Min: 25 K / Max: 25 K / Average: 25 K |
Image recording | Digitization - Scanner: PERKIN ELMER / Digitization - Sampling interval: 25 µm / Number real images: 24 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 17000 |
Sample stage | Specimen holder: Philips rotation-tilt holder / Specimen holder model: PHILIPS ROTATION HOLDER / Tilt series - Axis1 - Min angle: 4.3 ° / Tilt series - Axis1 - Max angle: 59.4 ° / Tilt series - Axis1 - Angle increment: 10 ° |
-Image processing
Details | Double axis tilt series collected on film. Digitized on PDS 1010M densitometer. Other relevent references K. A. Taylor, M. C. Reedy, L. Cordova and M. K. Reedy. 3-D structure of insect flight muscle in rigor from tilted thin sections. Nature 310, 28 5-291 (1984). Hanspeter Winkler and Kenneth A. Taylor. Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle. Ultramicroscopy 77, 141-152 (1999). Chen, Li Fan, Winkler, Hanspeter, Reedy, Michael K., Ree dy, Mary C. and Taylor, Kenneth A.. Molecular Modeling of Averaged Rigor Crossbridges from Tomograms of Insect Flight Muscle. J. Struct. Biol. 138(2), 92-104 (2002) |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER Details: The reconstruction was done by aligning the members of the tilt series using crosscorrelation functions, such as phase only and the VanHeel Mutual Correlation Function. The sampling in each ...Details: The reconstruction was done by aligning the members of the tilt series using crosscorrelation functions, such as phase only and the VanHeel Mutual Correlation Function. The sampling in each micrographof a tilted specimen was match by interpolation to th e lower angle members of the tilt series. This matching of areas and sampling was done by a 4 parameter grid search. Once aligned and scaled, the data were combined in Fourier space using a Whittaker-Shannon interpolation scheme. The map was calculated using a reverse Fourier transformation. The software used for the reconstruction was in-house and adapted from in some cases from MRC software. Number images used: 30 |
CTF correction | Details: none |
-Atomic model buiding 1
Software | Name: RSref |
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Details | Protocol: real space rigid body. Domains were fit manually into the density using O. The entire light chain domain consisting of heavy chain residues from G710 to K843 and the two light chains were repositioned using G710 of the myosin heavy chain using O.Real space refinement done using 7 rigid bodies and 4 hinge points. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT Target criteria: poor atom-atom contacts and cross correlation coefficient |
Output model | PDB-1m8q: PDB-1mvw: PDB-1o18: PDB-1o19: PDB-1o1a: PDB-1o1b: PDB-1o1c: PDB-1o1d: PDB-1o1e: PDB-1o1f: PDB-1o1g: |