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- PDB-5tby: HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF OBTAI... -

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Entry
Database: PDB / ID: 5tby
TitleHUMAN 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)
Components
  • Myosin light chain 3
  • Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
  • Myosin-7
KeywordsCONTRACTILE PROTEIN / CONTRACTILE PROTEIN Hypertrophic or dilated cardiomyopathy beta-cardiac myosin II Myosin interacting-heads motif
Function / homologyEF-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 sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 20 Å resolution
AuthorsALAMO, L. / WARE, J.S. / PINTO, A. / GILLILAN, R.E. / SEIDMAN, J.G. / SEIDMAN, C.E. / PADRON, R.
CitationJournal: 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/
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 13, 2016 / Release: Jun 7, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 7, 2017Structure modelrepositoryInitial release
1.1Jun 28, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Aug 9, 2017Structure modelDatabase referencespdbx_related_exp_data_set
1.3Sep 20, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.4Nov 8, 2017Structure modelDerived calculationspdbx_struct_assembly_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
1.5Jul 18, 2018Structure modelData collectionem_software_em_software.name
1.6Oct 3, 2018Structure modelData collection / Refinement descriptionrefine_refine.pdbx_refine_id
Remark 0This 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.

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-2240
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2240
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-2240
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Myosin-7
B: Myosin-7
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


Theoretical massNumber of molelcules
Total (without water)528,4436
Polyers528,4436
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)29570
ΔGint (kcal/M)-132
Surface area (Å2)137070
Helical symmetryNumber of operations: 3 / Rise per n subunits: 145 Å / Rotation per n subunits: 30 deg.

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Components

#1: Protein/peptide Myosin-7 / / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


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
#2: Protein/peptide Myosin light chain 3 / / Cardiac myosin light chain 1 / CMLC1 / Myosin light chain 1 / slow-twitch muscle B/ventricular isoform / MLC1SB / Ventricular myosin alkali light chain / Ventricular myosin light chain 1 / VLCl / Ventricular/slow twitch myosin alkali light chain / MLC-lV/sb


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
#3: Protein/peptide Myosin regulatory light chain 2, ventricular/cardiac muscle isoform / MLC-2v / Cardiac myosin light chain 2 / Myosin light chain 2 / slow skeletal/ventricular muscle isoform / MLC-2s/v / Ventricular myosin light chain 2


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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, 2, 3 / Source: NATURAL
Source (natural)Cellular location: SARCOPLASM / Organ: LEG / Organelle: THICK FILAMENTS / Organism: Aphonopelma (spider) / Tissue: MUSCLE
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer ID
1100 MMSodium ChlorideNaCl1
23 MMMagnesium ChlorideMgCl21
31 MMTriethylene glycol diamine tetraacetic acid (EGTA)C14H24N2O101
45 MMPIPESC8H18N2O6S21
55 MMSodium dihydrogen phosphateNAH2PO41
63 MMSdium AzideNAN31
SpecimenDetails: 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 supportDetails: 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
VitrificationInstrument: 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.

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Electron microscopy imaging

MicroscopyMicroscope 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 gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 90 kelvins / Temperature (min): 88 kelvins
Image recordingElectron 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 scansSampling size: 8.47 microns / Width: 250 / Height: 250

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectionHELIXBOXER
7UCSF Chimera10model fittingTHE "FIT IN MAP" TOOL WAS USED WITH DEFAULT OPTIONS
13ITERATIVE HELICAL REAL SPACE RECONSTRUCTION (EGELMAN, 2000)SPIDER 143D reconstructionmodification of the IHRSR method
Image processingDetails: 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 correctionType: NONE
Particle selectionDetails: 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
SymmetryPoint symmetry: C4
3D reconstructionResolution: 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 buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: CORRELATION COEFFICIENT
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range
13JBH

3jbh

A11-962
23JBH

3jbh

B11-962
33JBH

3jbh

C11-156
43JBH

3jbh

D11-156
53JBH

3jbh

E11-196
63JBH

3jbh

F11-196
Least-squares processHighest resolution: 2 Å

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