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- EMDB-1001: Real space refinement of acto-myosin structures from sectioned muscle. -

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Entry
Database: EMDB / ID: EMD-1001
TitleReal space refinement of acto-myosin structures from sectioned muscle.
Map dataActo-myosin structures from sectioned muscle
Sample
  • Sample: Rigor insect flight muscle from Lethocerus maximus
  • Organelle or cellular component: thick, myosin-containing filament
  • Organelle or cellular component: thin, actin-containing filament
Function / homology
Function and homology information


regulation of myosin II filament assembly / contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin complex / myosin II complex / cytoskeletal motor activator activity / myosin heavy chain binding / microfilament motor activity / tropomyosin binding ...regulation of myosin II filament assembly / contractile muscle fiber / Striated Muscle Contraction / myosin filament / myosin complex / myosin II complex / cytoskeletal motor activator activity / myosin heavy chain binding / microfilament motor activity / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / myofibril / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle tissue development / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / muscle contraction / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament 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
: / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...: / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / ATPase, nucleotide binding domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 1, skeletal muscle isoform / Myosin light chain 3, skeletal muscle isoform / Myosin regulatory light chain 11 / Myosin heavy chain, skeletal muscle, adult / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesLethocerus (insect)
Methodelectron tomography / negative staining / Resolution: 40.0 Å
AuthorsChen LF / Blanc E / Chapman MS / Taylor KA
CitationJournal: 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
DepositionJun 18, 2002-
Header (metadata) releaseJun 20, 2002-
Map releaseJun 20, 2002-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: PDBe / Status: Released

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1001.gif

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Map

FileDownload / File: emd_1001.map.gz / Format: CCP4 / Size: 40.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActo-myosin structures from sectioned muscle
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
15.47 Å/pix.
x 30 pix.
= 464. Å		15.47 Å/pix.
x 600 pix.
= 9280. Å		15.47 Å/pix.
x 600 pix.
= 9280. Å

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generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 15.4667 Å
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Contour Level1: 81.200000000000003
Minimum - Maximum-417.992000000000019 - 366.680000000000007
Average (Standard dev.)1.85973 (±47.791600000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-15
Dimensions60060030
Spacing60060030
CellA: 9280 Å / B: 9280 Å / C: 464 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z15.46666666666715.46666666666715.466666666667
M x/y/z60060030
origin x/y/z0.0000.0000.000
length x/y/z9280.0009280.000464.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-15
NC/NR/NS60060030
D min/max/mean-417.992366.6801.860

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Sample components

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Entire : Rigor insect flight muscle from Lethocerus maximus

EntireName: Rigor insect flight muscle from Lethocerus maximus
Components
  • Sample: Rigor insect flight muscle from Lethocerus maximus
  • Organelle or cellular component: thick, myosin-containing filament
  • Organelle or cellular component: thin, actin-containing filament

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Supramolecule #1000: Rigor insect flight muscle from Lethocerus maximus

SupramoleculeName: 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

SupramoleculeName: 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
Source (natural)Organism: Lethocerus (insect) / synonym: water bug, Lethocerus maximus / Tissue: Indirect flight muscles / Cell: muscle fibers / Organelle: myofibrils / Location in cell: myofibrils

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Supramolecule #2: thin, actin-containing filament

SupramoleculeName: 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
Source (natural)Organism: Lethocerus (insect) / synonym: water bug, Lethocerus maximus / Tissue: Indirect flight muscles / Cell: Muscle fibers / Organelle: myofibrils / Location in cell: myofibrils

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography

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Sample preparation

VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI/PHILIPS EM400
TemperatureMin: 25 K / Max: 25 K / Average: 25 K
Image recordingDigitization - Scanner: PERKIN ELMER / Digitization - Sampling interval: 25 µm / Number real images: 24 / Bits/pixel: 16
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 17000
Sample stageSpecimen 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 °

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Image processing

DetailsDouble 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)
Final reconstructionAlgorithm: 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 correctionDetails: none

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Atomic model buiding 1

SoftwareName: RSref
DetailsProtocol: 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Target criteria: poor atom-atom contacts and cross correlation coefficient
Output model

PDB-1m8q:
Molecular Models of Averaged Rigor Crossbridges from Tomograms of Insect Flight Muscle

PDB-1mvw:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o18:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o19:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1a:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1b:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1c:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1d:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1e:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1f:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

PDB-1o1g:
MOLECULAR MODELS OF AVERAGED RIGOR CROSSBRIDGES FROM TOMOGRAMS OF INSECT FLIGHT MUSCLE

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