|Entry||Database: PDB / ID: 5tby|
|Title||HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF OBTAINED BY HOMOLOGY MODELING (USING SWISS-MODEL) OF HUMAN SEQUENCE FROM APHONOPELMA HOMOLOGY MODEL (PDB-3JBH), RIGIDLY FITTED TO HUMAN BETA-CARDIAC NEGATIVELY STAINED THICK FILAMENT 3D-RECONSTRUCTION (EMD-2240)|
|Keywords||CONTRACTILE PROTEIN / CONTRACTILE PROTEIN Hypertrophic or dilated cardiomyopathy beta-cardiac myosin II Myosin interacting-heads motif|
|Function / homology||EF-Hand 1, calcium-binding site / Myosin N-terminal SH3-like domain / Myosin IQ motif-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Myosin, N-terminal, SH3-like / Kinesin motor domain superfamily / Myosin tail / Myosin head (motor domain) / Myosin tail / EF-hand domain ...EF-Hand 1, calcium-binding site / Myosin N-terminal SH3-like domain / Myosin IQ motif-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Myosin, N-terminal, SH3-like / Kinesin motor domain superfamily / Myosin tail / Myosin head (motor domain) / Myosin tail / EF-hand domain / EF-hand domain / EF-hand domain pair / EF-hand calcium-binding domain. / IQ motif profile. / EF-hand calcium-binding domain profile. / Myosin motor domain profile. / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Striated Muscle Contraction / IQ motif, EF-hand binding site / Myosin S1 fragment, N-terminal / myosin II heavy chain binding / regulation of slow-twitch skeletal muscle fiber contraction / muscle cell fate specification / regulation of the force of skeletal muscle contraction / adult heart development / muscle fiber development / cardiac myofibril / regulation of the force of heart contraction / cardiac myofibril assembly / positive regulation of the force of heart contraction / cardiac muscle hypertrophy in response to stress / transition between fast and slow fiber / muscle myosin complex / regulation of striated muscle contraction / A band / positive regulation of ATPase activity / actin-dependent ATPase activity / myosin filament / skeletal muscle contraction / microfilament motor activity / striated muscle contraction / muscle filament sliding / myosin complex / structural constituent of muscle / I band / myofibril / heart contraction / myosin heavy chain binding / ventricular cardiac muscle tissue morphogenesis / ATP metabolic process / actin monomer binding / cardiac muscle contraction / motor activity / skeletal muscle tissue development / stress fiber / sarcomere / post-embryonic development / regulation of heart rate / muscle contraction / Z disc / negative regulation of cell growth / actin filament binding / heart development / ATPase activity / calmodulin binding / cytoskeleton / calcium ion binding / ATP binding / cytosol / Myosin light chain 3 / Myosin regulatory light chain 2, ventricular/cardiac muscle isoform / Myosin-7|
Function and homology information
|Specimen source||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 20 Å resolution|
|Authors||ALAMO, L. / WARE, J.S. / PINTO, A. / GILLILAN, R.E. / SEIDMAN, J.G. / SEIDMAN, C.E. / PADRON, R.|
|Citation||Journal: Bioinformatics / Year: 2006|
Title: The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
Authors: Konstantin Arnold / Lorenza Bordoli / Jürgen Kopp / Torsten Schwede
Abstract: MOTIVATION: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology ...MOTIVATION: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases.
RESULTS: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3.
AVAILABILITY: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/
SummaryFull reportAbout validation report
|Date||Deposition: Sep 13, 2016 / Release: Jun 7, 2017|
|Remark 0||This entry reflects an alternative modeling of the original data in 3JBH, determined by ALAMO, L., ...This entry reflects an alternative modeling of the original data in 3JBH, determined by ALAMO, L., QI, D., WRIGGERS, W., PINTO, A., ZHU, J., BILBAO, A., GILLILAN, R.E., HU, S., PADRON, R.|
|Structure viewer||Molecule: |
Downloads & links
C: Myosin light chain 3
D: Myosin light chain 3
E: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
F: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
|Helical symmetry||Number of operations: 3 / Rise per n subunits: 145 Å / Rotation per n subunits: 30 deg.|
Mass: 223445.984 Da / Num. of mol.: 2
Details: MYOSIN 2 HEAVY CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC ...MYOSIN 2 HEAVY CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
Fragment: SUBFRAGMENT 1(S1) / Source: (natural) Homo sapiens (human) / References: UniProt: P12883
Mass: 21962.068 Da / Num. of mol.: 2
Details: MYOSIN 2 ESSENTIAL LIGHT CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE (CHAIN C) AND BLOCKED (CHAIN D) ...MYOSIN 2 ESSENTIAL LIGHT CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE (CHAIN C) AND BLOCKED (CHAIN D) HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
Source: (natural) Homo sapiens (human) / References: UniProt: P08590
Mass: 18813.273 Da / Num. of mol.: 2
Details: MYOSIN 2 REGULATORY LIGHT CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE (CHAIN E) AND BLOCKED (CHAIN F) ...MYOSIN 2 REGULATORY LIGHT CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE (CHAIN E) AND BLOCKED (CHAIN F) HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
Source: (natural) Homo sapiens (human) / References: UniProt: P10916
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: single particle reconstruction|
|Component||Name: MYOSIN THICK FILAMENTS TARANTULA STRIATED MUSCLE / Type: TISSUE|
Details: THE ATOMIC MODEL CONSIST OF ONE INTERACTING-HEADS MOTIF, FORMED BY TWO HEAVY MEROMYOSIN (S1 MYOSIN HEAD WITH A SEGMENT OF S2 AND ESSENTIAL AND REGULATORY LIGHT CHAINS) SO CALLED BLOCKED AND FREE HEADS, THE HOMOLOGY MODEL IS BASED ON TARANTULA STRIATED MUSCLE MODEL STRUCTURE 3JBH. THIS MODEL WAS RIGIDLY DOCKED TO A TARANTULA 3D MAP (EMD-1950) AND ALSO AGAINST HUMAN BETA-CARDIAC NEGATIVELY STAINED THICK FILAMENT 2.8 NM RESOLUTION 3D-RECONSTRUCTION (EMD-2240)
Entity ID: 1,
|Source (natural)||Cellular location: SARCOPLASM / Organ: LEG / Organelle: THICK FILAMENTS / Organism: Aphonopelma (spider) / Tissue: MUSCLE||Buffer solution||pH: 7||Buffer component|
|Specimen||Details: A 6 ul aliquot of native purified tarantula thick filaments suspension (Hidalgo et al. 2001).|
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Specimen support||Details: Holey carbon grids had been rendered hydrophilic by glow discharge in n-amylamine vapor for 3 minutes before use.|
Grid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 296 kelvins|
Details: PLUNGING IN A LIQUID ETHANE COOLED BY LIQUID NITROGEN. BLOTTING WAS PERFORMED FROM ONE SIDE OF THE GRID TILL A THIN SAMPLE FILM ON IT USING WHATMAN NO. 42 FILTER PAPER, THEN THE GRID WAS IMMEDIATELY PLUNGED UNDER GRAVITY INTO LIQUID ETHANE COOLED BY LIQUID NITROGEN. GRIDS WERE STORED UNDER LIQUID NITROGEN.
-Electron microscopy imaging
|Microscopy||Microscope model: FEI/PHILIPS CM120T|
Details: Holey carbon grids Cryopreserved in Liquid ethane were observed in a Philips CM120 electron microscope under low dose conditions. Only filaments on thin carbon over holes were photographed
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 35000 / Calibrated magnification: 35000 / Nominal defocus max: 1950 nm / Nominal defocus min: 1950 nm / Calibrated defocus min: 1950 nm / Calibrated defocus max: 1950 nm / Cs: 2 mm / Alignment procedure: BASIC|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 90 kelvins / Temperature (min): 88 kelvins|
|Image recording||Electron dose: 9 e/Å2|
Details: Low-dose electron micrographs of 1008 frozen-hydrated thick filaments halves ere digitized at 0.248 nm per pixel using a Nikon Super Coolscan 8000 ED scanner.
Film or detector model: KODAK SO-163 FILM / Number of real images: 500
|Image scans||Sampling size: 8.47 microns / Width: 250 / Height: 250|
|Image processing||Details: Three-dimensional single particle reconstruction was carried out by a modification of the IHRSR method, using SPIDER. Low-dose electron micrographs of 1008 frozen-hydrated thick filaments halves where digitized at 0.248 nm per pixel using a Nikon Super Coolscan 8000 ED scanner. Filaments were aligned with the bare zone at the top, to ensure correct polarity in subsequent steps.|
|CTF correction||Type: NONE|
|Particle selection||Details: A total of 15,504 segments, each 62 nm long, with an overlap of 55.8 nm, and containing aprox. 40,000 unique pairs of interacting myosin heads went into the reconstruction.|
Number of particles selected: 15504
|Symmetry||Point symmetry: C4|
|3D reconstruction||Resolution: 20 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 10700 / Algorithm: BACK PROJECTION|
Details: For projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus 12 deg. every 2deg., 45 reference rotated projections (0-90 degrees, 2deg. rotation angle), and 7 image axial shifts of 2.2 nm. The resulting 3D-map combines about 10,700 out of 15,504 filament segments, a yield of 69 percent of included segments. There are 4 helices of myosin heads, rotated 30 degrees, every 145 Angstroms. The filament segments were selected based on visual judgement of good helical order.
Number of class averages: 4095 / Symmetry type: POINT
|Atomic model building||Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: CORRELATION COEFFICIENT|
|Atomic model building|
|Least-squares process||Highest resolution: 2 Å|
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