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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)

by single particle reconstruction, at 20 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on simplified surface model of EM map, EMDB-2240, Imaged by Jmol

#3: Superimposition on EM map, EMDB-2240, Imaged by UCSF CHIMERA

#4: Superimposition on EM map, EMDB-2240, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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)
DescriptorMyosin-7
Myosin light chain 3
Myosin regulatory light chain 2
ventricular/cardiac muscle isoform
KeywordsCONTRACTILE PROTEIN, CONTRACTILE PROTEIN Hypertrophic or dilated cardiomyopathy beta-cardiac myosin II Myosin interacting-heads motif
AuthorsALAMO, L., WARE, J.S., PINTO, A., GILLILAN, R.E., SEIDMAN, J.G., SEIDMAN, C.E., PADRON, R.
DateDeposition: 2016-09-13, Release: 2017-06-07
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on simplified surface model of EM map, EMDB-2240, Imaged by Jmol

#3: Superimposition on EM map, EMDB-2240, Imaged by UCSF CHIMERA

#4: Superimposition on EM map, EMDB-2240, Imaged by UCSF CHIMERA

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Article
Citation - primary
ArticleElife, Vol. 6, Year 2017
TitleEffects of myosin variants on interacting-heads motif explain distinct hypertrophic and dilated cardiomyopathy phenotypes.
AuthorsLorenzo Alamo, James S Ware, Antonio Pinto, Richard E Gillilan, Jonathan G Seidman, Christine E Seidman, Raúl Padrón
Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.
National Heart and Lung Institute and MRC London Institute for Medical Sciences, Imperial College London, London, United Kingdom.
NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, United Kingdom.
Department of Genetics, Harvard Medical School, Boston, United States.
Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source, Ithaca, United States.
Cardiovascular Division, Brigham and Women's Hospital and Howard Hughes Medical Institute, Boston, United States.
LinksPubMed: 28606303, DOI: 10.7554/eLife.24634, PMC: PMC5469618
Citation - original_data_1
ArticleJ. Mol. Biol., Vol. 428, Issue 6, Page 1142-1164, Year 2016
TitleConserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.
AuthorsLorenzo Alamo, Dan Qi, Willy Wriggers, Antonio Pinto, Jingui Zhu, Aivett Bilbao, Richard E Gillilan, Songnian Hu, Raúl Padrón
Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020A, Venezuela.
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
Department of Mechanical and Aerospace Engineering, Old Dominion University, 5115 Hampton Boulevard, Norfolk, VA 23529, USA.
Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source, 161 Wilson Laboratory, Synchrotron Drive, Ithaca, NY 14853, USA.
KeywordsAnimals, Cryoelectron Microscopy, Imaging, Three-Dimensional, Models, Molecular, Myosins (chemistry, 3.6.4.1), Protein Conformation, Protein Interaction Mapping, Spiders
LinksPubMed: 26851071, PII: S0022-2836(16)00082-6, DOI: 10.1016/j.jmb.2016.01.027, PMC: PMC4826325
Citation - 1
ArticleJ. Mol. Biol., Vol. 384, Issue 4, Page 780-797, Year 2008
TitleThree-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.
AuthorsLorenzo Alamo, Willy Wriggers, Antonio Pinto, Fulvia Bártoli, Leiria Salazar, Fa-Qing Zhao, Roger Craig, Raúl Padrón
Departamento de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.
KeywordsAnimals, Crystallography, X-Ray, Microscopy, Electron, Transmission, Models, Molecular, Molecular Sequence Data, Myosin Light Chains (genetics), Myosins (chemistry, 3.6.4.1), Phosphorylation, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Analysis, DNA, Spiders (chemistry)
LinksPubMed: 18951904, PII: S0022-2836(08)01285-0, DOI: 10.1016/j.jmb.2008.10.013, PMC: PMC2729561
Citation - 2
ArticleJ. Mol. Biol., Vol. 428, Issue 6, Page 1142-1164, Year 2016
TitleConserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.
AuthorsLorenzo Alamo, Dan Qi, Willy Wriggers, Antonio Pinto, Jingui Zhu, Aivett Bilbao, Richard E Gillilan, Songnian Hu, Raúl Padrón
Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020A, Venezuela.
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
Department of Mechanical and Aerospace Engineering, Old Dominion University, 5115 Hampton Boulevard, Norfolk, VA 23529, USA.
Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source, 161 Wilson Laboratory, Synchrotron Drive, Ithaca, NY 14853, USA.
KeywordsAnimals, Cryoelectron Microscopy, Imaging, Three-Dimensional, Models, Molecular, Myosins (chemistry, 3.6.4.1), Protein Conformation, Protein Interaction Mapping, Spiders
LinksPubMed: 26851071, PII: S0022-2836(16)00082-6, DOI: 10.1016/j.jmb.2016.01.027, PMC: PMC4826325
Citation - 3
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 110, Issue 1, Page 318-323, Year 2013
TitleAtomic model of the human cardiac muscle myosin filament.
AuthorsHind A Al-Khayat, Robert W Kensler, John M Squire, Steven B Marston, Edward P Morris
National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.
KeywordsCarrier Proteins (metabolism), Connectin, Crystallography, X-Ray, Humans, Imaging, Three-Dimensional, Microscopy, Electron, Models, Molecular, Muscle Proteins (metabolism), Myocardium (chemistry), Myofibrils (chemistry), Myosins (chemistry, 3.6.4.1), Protein Kinases (metabolism, 2.7.-), TTN protein, human, myosin-binding protein C
LinksPubMed: 23251030, DOI: 10.1073/pnas.1212708110, PMC: PMC3538242
Citation - 4
ArticleElectrophoresis, Vol. 18, Issue 15, Page 2714-2723, Year 1997
TitleSWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
AuthorsN Guex, M C Peitsch
Geneva Biomedical Research Institute, Glaxo Wellcome Research and Development, Plan-les-Ouates/Geneva, Switzerland.
KeywordsAmino Acid Sequence, Automation, Databases, Factual, Models, Molecular, Molecular Sequence Data, Reproducibility of Results, Sequence Homology, Amino Acid
LinksPubMed: 9504803, DOI: 10.1002/elps.1150181505
Citation - 5
ArticleNucleic Acids Res., Vol. 31, Issue 13, Page 3381-3385, Year 2003
TitleSWISS-MODEL: An automated protein homology-modeling server.
AuthorsTorsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C Peitsch
Biozentrum der Universität Basel, Klingelbergstr. 50-70, CH 4056 Basel, Switzerland.
KeywordsComputer Graphics, Internet, Models, Molecular, Proteins (chemistry), Sequence Alignment, Sequence Analysis, Protein, Software, Structural Homology, Protein, User-Computer Interface
LinksPubMed: 12824332, PMC: PMC168927
Citation - 6
ArticleBioinformatics, Vol. 22, Issue 2, Page 195-201, Year 2006
TitleThe SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
AuthorsKonstantin Arnold, Lorenza Bordoli, Jürgen Kopp, Torsten Schwede
Biozentrum Basel, University of Basel Switzerland.
KeywordsAlgorithms, Amino Acid Sequence, Computer Simulation, Databases, Protein, Internet, Models, Chemical, Models, Molecular, Molecular Sequence Data, Online Systems, Protein Conformation, Proteins (analysis), Sequence Alignment (methods), Sequence Analysis, Protein (methods), Sequence Homology, Amino Acid, Software, Systems Integration, User-Computer Interface
LinksPubMed: 16301204, DOI: 10.1093/bioinformatics/bti770
Components
ID 1 : Myosin heavy chain 7,Myosin heavy chain slow isoform,MyHC-slow,Myosin heavy chain,cardiac muscle beta isoform,MyHC-beta
DescriptionMyosin-7
Typepolypeptide(L)
FragmentSUBFRAGMENT 1(S1)
Formula weight223445.984 Da
Number of molecules2
ID1
DetailsMYOSIN 2 HEAVY CHAIN, VENTRICULAR CARDIAC MUSCLE, FREE HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 1935
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P12883, Sequence view
ID 2 : 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
DescriptionMyosin light chain 3
Typepolypeptide(L)
Formula weight21962.068 Da
Number of molecules2
ID2
DetailsMYOSIN 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
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 195
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P08590, Sequence view
ID 3 : MLC-2v,Cardiac myosin light chain 2,Myosin light chain 2,slow skeletal/ventricular muscle isoform,MLC-2s/v,Ventricular myosin light chain 2
DescriptionMyosin regulatory light chain 2, ventricular/cardiac muscle isoform
Typepolypeptide(L)
Formula weight18813.273 Da
Number of molecules2
ID3
DetailsMYOSIN 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
SourceMethod: Isolated from a natural source
Src id: 1
Common name: Human
Alt source flag: sample
Beg seq num: 1
End seq num: 166
NCBI taxonomy: ID:9606
Organism scientific: Homo sapiens
LinksUniProt: P10916, Sequence view
Sample
Entity assembly
DetailsTHE 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 list1, 2, 3
NameMYOSIN THICK FILAMENTS TARANTULA STRIATED MUSCLE
SourceNATURAL
TypeTISSUE
Buffer
Specimen id1
PH7.0
Experiment
Aggregation stateFILAMENT
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
DetailsHoley carbon grids had been rendered hydrophilic by glow discharge in n-amylamine vapor for 3 minutes before use.
Grid materialCOPPER
Grid mesh size400
Grid typeQuantifoil
Vitrification
Specimen id1
Chamber temperature296
Cryogen nameETHANE
DetailsPLUNGING 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.
Humidity80
InstrumentHOMEMADE PLUNGER
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM120T
DetailsHoley 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 sourceLAB6
Accelerating voltage120 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 35000 X, Nominal: 35000 X
CsNominal: 2.0 mm
Nominal defocusMax: 1950 nm, Min: 1950 nm
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN
Recording temperatureMaximum: 90, Minimum: 88
Image scans
Image recording id1
Dimension height250
Dimension width250
Sampling size8.47
Processing
Single particle entity
Image processing id1
Point symmetryC4
3D reconstruction
Image processing id1
AlgorithmBACK PROJECTION
DetailsFor 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.
Num class averages4095
Number of particles10700
Resolution20 A
Resolution methodFSC 0.5 CUT-OFF
Symmetry typePOINT
3D fitting
Refinement ProtocolRIGID BODY FIT
Refinement SpaceREAL
Target criteriaCORRELATION COEFFICIENT
3D fitting list
3D Fitting ID1
Pdb chain idA
Pdb chain residue range1-962
PDB entry ID3JBH
3D fitting list
3D Fitting ID1
Pdb chain idB
Pdb chain residue range1-962
PDB entry ID3JBH
3D fitting list
3D Fitting ID1
Pdb chain idC
Pdb chain residue range1-156
PDB entry ID3JBH
3D fitting list
3D Fitting ID1
Pdb chain idD
Pdb chain residue range1-156
PDB entry ID3JBH
3D fitting list
3D Fitting ID1
Pdb chain idE
Pdb chain residue range1-196
PDB entry ID3JBH
3D fitting list
3D Fitting ID1
Pdb chain idF
Pdb chain residue range1-196
PDB entry ID3JBH
Refine
Refine id1
Ls d res high20.00 A
Download
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mmCIF5tby.cif.gz
XML format
All5tby.xml.gz
No-atom5tby-noatom.xml.gz
Ext-atom5tby-extatom.xml.gz
Movie files
movie #1
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movie #2
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movie #3
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movie #4
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