[English] 日本語
Yorodumi
- PDB-5tby: HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF OBTAI... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

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)
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
Specimen sourceHomo sapiens / human
MethodElectron microscopy (20 Å resolution / Filament / Single particle)
AuthorsALAMO, L. / WARE, J.S. / PINTO, A. / GILLILAN, R.E. / SEIDMAN, J.G. / SEIDMAN, C.E. / PADRON, R.
CitationElife, 2017, 6

primary. Elife, 2017, 6 StrPapers
Effects of myosin variants on interacting-heads motif explain distinct hypertrophic and dilated cardiomyopathy phenotypes.
Lorenzo Alamo / James S Ware / Antonio Pinto / Richard E Gillilan / Jonathan G Seidman / Christine E Seidman / Raúl Padrón

original_data_1. J. Mol. Biol., 2016, 428, 1142-1164 StrPapers
Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.
Alamo, L. / Qi, D. / Wriggers, W. / Pinto, A. / Zhu, J. / Bilbao, A. / Gillilan, R.E. / Hu, S. / Padron, R.

#1. J. Mol. Biol., 2008, 384, 780-797 StrPapers
Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.
Alamo, L. / Wriggers, W. / Pinto, A. / Bartoli, F. / Salazar, L. / Zhao, F.Q. / Craig, R. / Padron, R.

#2. J. Mol. Biol., 2016, 428, 1142-1164 StrPapers
Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.
Alamo, L. / Qi, D. / Wriggers, W. / Pinto, A. / Zhu, J. / Bilbao, A. / Gillilan, R.E. / Hu, S. / Padron, R.

#3. Proc. Natl. Acad. Sci. U.S.A., 2013, 110, 318-323 StrPapers
Atomic model of the human cardiac muscle myosin filament.
Al-Khayat, H.A. / Kensler, R.W. / Squire, J.M. / Marston, S.B. / Morris, E.P.

#4. Electrophoresis, 1997, 18, 2714-2723 StrPapers
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
Guex, N. / Peitsch, M.C.

#5. Nucleic Acids Res., 2003, 31, 3381-3385 StrPapers
SWISS-MODEL: An automated protein homology-modeling server.
Schwede, T. / Kopp, J. / Guex, N. / Peitsch, M.C.

#6. Bioinformatics, 2006, 22, 195-201 StrPapers
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.
Arnold, K. / Bordoli, L. / Kopp, J. / Schwede, T.

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
Remark 0This 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 visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
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
MethodPISA

-
Components

#1: Polypeptide(L)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 HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
Fragment: SUBFRAGMENT 1(S1) / Source: (natural) Homo sapiens / human / References: UniProt: P12883
#2: Polypeptide(L)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) HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
Source: (natural) Homo sapiens / human / References: UniProt: P08590
#3: Polypeptide(L)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) HEAD HOMOLOGY MODEL OF HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF
Source: (natural) Homo sapiens / human / References: UniProt: P10916

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

-
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 / Tissue: MUSCLE
Buffer solutionpH: 7
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1100MMSodium ChlorideNaCl1
23MMMagnesium ChlorideMgCl21
31MMTriethylene glycol diamine tetraacetic acid (EGTA)C14H24N2O101
45MMPIPESC8H18N2O6S21
55MMSodium dihydrogen phosphateNAH2PO41
63MMSdium 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.

-
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 FIELD / 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 / Dimension width: 250 / Dimension height: 250

-
Processing

EM software
IDNameVersionCategoryDetailsImage processing IDFitting ID
1EMAN2PARTICLE SELECTIONHELIXBOXER1
7CHIMERA10MODEL FITTINGTHE "FIT IN MAP" TOOL WAS USED WITH DEFAULT OPTIONS1
13ITERATIVE HELICAL REAL SPACE RECONSTRUCTION (EGELMAN, 2000)SPIDER 14RECONSTRUCTIONmodification of the IHRSR method1
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more