[English] 日本語
Yorodumi
- PDB-3jax: Heavy meromyosin from Schistosoma mansoni muscle thick filament b... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3jax
TitleHeavy meromyosin from Schistosoma mansoni muscle thick filament by negative stain EM
Descriptormyosin 2 heavy chain
smooth muscle myosin essential light chain
myosin regulatory light chain
KeywordsCONTRACTILE PROTEIN / muscle protein / smooth muscle / myosin subfragment 2 / heavy meromyosin / essential light chain / regulatory light chain / motor protein / coiled-coil
Specimen sourceSchistosoma mansoni / invertebrata / blood fluke / マンソン住血吸虫 /
MethodElectron microscopy (23 Å resolution / Filament / Helical)
AuthorsSulbaran, G. / Alamo, L. / Pinto, A. / Marquez, G. / Mendez, F. / Padron, R. / Craig, R.
CitationProc. Natl. Acad. Sci. U.S.A., 2015, 112, E5660-E5668

primary. Proc. Natl. Acad. Sci. U.S.A., 2015, 112, E5660-E5668 Yorodumi Papers
An invertebrate smooth muscle with striated muscle myosin filaments.
Guidenn Sulbarán / Lorenzo Alamo / Antonio Pinto / Gustavo Márquez / Franklin Méndez / Raúl Padrón / Roger Craig

#1. J.Mol.Biol., 2008, 384, 780-797 Yorodumi Papers
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., 2003, 329, 963-972 Yorodumi Papers
Refined model of the 10S conformation of smooth muscle myosin by cryo-electron microscopy 3D image reconstruction.
Liu, J. / Wendt, T. / Taylor, D. / Taylor, K.

#3. Proc.Natl.Acad.Sci.USA, 2006, 103, 17713-17717 Yorodumi Papers
Crystal structures of human cardiac beta-myosin II S2-Delta provide insight into the functional role of the S2 subfragment.
Blankenfeldt, W. / Thoma, N.H. / Wray, J.S. / Gautel, M. / Schlichting, I.

#4. Cell(Cambridge,Mass.), 1999, 97, 459-470 Yorodumi Papers
Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head.
Houdusse, A. / Kalabokis, V.N. / Himmel, D. / Szent-Gyorgyi, A.G. / Cohen, C.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2015 / Release: Oct 7, 2015
RevisionDateData content typeGroupProviderType
1.0Oct 7, 2015Structure modelrepositoryInitial release
1.1Oct 21, 2015Structure modelDatabase references
1.2Nov 4, 2015Structure modelDatabase references

-
Structure visualization

Movie
  • Biological unit as representative helical assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6370
  • 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 2 heavy chain
B: myosin 2 heavy chain
C: smooth muscle myosin essential light chain
D: smooth muscle myosin essential light chain
E: myosin regulatory light chain
F: myosin regulatory light chain


Theoretical massNumber of molelcules
Total (without water)301,7926
Polyers301,7926
Non-polymers00
Water0
#1
A: myosin 2 heavy chain
B: myosin 2 heavy chain
C: smooth muscle myosin essential light chain
D: smooth muscle myosin essential light chain
E: myosin regulatory light chain
F: myosin regulatory light chain
x 20


Theoretical massNumber of molelcules
Total (without water)6,035,839120
Polyers6,035,839120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation20
#2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
#3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1

-
Components

#1: Polypeptide(L)myosin 2 heavy chain


Mass: 112182.516 Da / Num. of mol.: 2
Source: (natural) Schistosoma mansoni / invertebrata / マンソン住血吸虫 /

Cellular component

Molecular function

#2: Polypeptide(L)smooth muscle myosin essential light chain


Mass: 17004.221 Da / Num. of mol.: 2
Source: (natural) Schistosoma mansoni / invertebrata / マンソン住血吸虫 /

Molecular function

#3: Polypeptide(L)myosin regulatory light chain


Mass: 21709.250 Da / Num. of mol.: 2
Source: (natural) Schistosoma mansoni / invertebrata / マンソン住血吸虫 /

Molecular function

Sequence detailsTHE IMAGED FILAMENTS ARE FROM SCHISTOSOMA MANSONI, BUT THE MODELED SEQUENCES ARE FROM CHICKEN/HUMAN CHIMERA (CHAINS A,B), CHICKEN (CHAINS C,D), AND TARANTULA (CHAINS E,F). SEQUENCE CONFLICTS FOR CHAINS A AND B ARE CONSISTENT WITH PDB ENTRIES 1BR1 AND 1I84. THE SEQUENCE OF THE HEAVY CHAIN STRUCTURE REPORTED HERE DIFFERS FROM THAT REPORTED IN UNP P10587. SER 2 TO ALA IS A CLONING ARTIFACT IN PDB ENTRY 1BR1. PEPTIDE CHAIN DESIGNATIONS: THE TERMS "BLOCKED" AND "FREE" REFER TO THE CONFORMATIONS OF THE TWO S1 MYOSIN HEADS. "FREE" MYOSIN HEAD MYOSIN HEAVY CHAIN S1 PLUS S2 FRAGMENT IS CHAIN A ELC IS CHAIN C RLC IS CHAIN E "BLOCKED" MYOSIN HEAD MYOSIN HEAVY CHAIN S1 PLUS S2 FRAGMENT IS CHAIN B ELC IS CHAIN D RLC IS CHAIN F SEQUENCE GAPS IN THE MOLECULAR MODEL: HEAVY CHAIN UNP P10587 CHAINS A AND B: 1, 205-210, 452-457, 635-655, 853-1979 HEAVY CHAIN S2 FRAGMENT UNP P12883 CHAIN A: 1-841, 962-1935 HEAVY CHAIN S2 FRAGMENT UNP P12883 CHAIN B: 1-841, 964-1935 ELC UNP P02607 CHAINS C AND D: 1-3

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

-
Sample preparation

Component
IDNameTypeDetailsParent ID
1Myosin thick filaments from Schistosoma mansoni smooth muscleCOMPLEXPolymer of myosin II molecules helically assembled over a paramyosin core0
2Myosin II1
Buffer solutionName: 100 mM NaCl, 3 mM MgCl2, 1 mM EGTA, 5 mM PIPES, 1mM NaN3, 5 mM MgATP, 0.01 mM blebbistatin, protease inhibitor cocktail (Sigma P-8465)
Details: 100 mM NaCl, 3 mM MgCl2, 1 mM EGTA, 5 mM PIPES, 1mM NaN3, 5 mM MgATP, 0.01 mM blebbistatin, protease inhibitor cocktail (Sigma P-8465)
pH: 7
SpecimenDetails: One drop of filament suspension was placed on grids and negatively stained with 1% uranyl acetate.
Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: 400-mesh holey carbon grids. Specimens were imaged on thin carbon extending over the holes.

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM120T / Date: Feb 15, 2013 / Details: 1.5 post-magnification, low-dose conditions
Electron gunElectron source: LAB6 / Accelerating voltage: 80 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 / Calibrated magnification: 42000 / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2 mm
Astigmatism: Objective lens astigmatism was corrected at 240,000 times magnification
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC / Specimen holder type: Room temperature holder
Image recordingElectron dose: 10 e/Å2 / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k)
Image scansNumber digital images: 263
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1UCSF ChimeraMODEL FITTING
2EMAN2RECONSTRUCTION
3SPIDERRECONSTRUCTION
Helical symmertyAngular rotation/subunit: 30 deg. / Axial rise/subunit: 145 Å / Axial symmetry: C4
Details: Heavy meromyosin (HMM) is the outermost helical unit of the myosin thick filament formed by two myosin heads that include the motor domains, the proteolytic fragment of myosin heavy chain subfragment 2 (S2), and two associated light chains (ELC and RLC).
3D reconstructionMethod: Single particle reconstruction with a modification of the IHRSR method
Resolution: 23 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 9500 / Nominal pixel size: 5.7 / Actual pixel size: 5.7
Details: For each iteration of reconstruction (30 cycles), filament segment projections were compared with different projections of the reference reconstruction as follows: seven 2.3 nm axial shifts, 2 degree intervals of rotation about the filament axis up to 90 degrees, and 2 degree intervals of out-of-plane tilting from -10 degrees to +10 degrees. The total number of projections was 7 x 45 x 11 = 3465. For the final 19 cycles of the reconstruction, we used only the best-ordered 420 filament halves (those in which >30% of the segments were found good enough to be used by the reconstruction script in the back-projection in previous cycles). From ~17,000 segments, ~9,500 (56%) were included in the final reconstruction. This final 3D-reconstruction was the average of the last 19 reconstructions between cycles 12 - 30. Its resolution, according to the 0.5 Fourier Shell Correlation (FSC) criterion, was 2.3 nm.
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--rigid docking REFINEMENT PROTOCOL--RIGID BODY DETAILS--3DTP was fitted as a rigid body using the Fit in Map tool of UCSF Chimera.
Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-IDPdb chain ID 3D fitting ID
13DTPA1
23DTPB1
33DTPC1
43DTPD1
53DTPE1
63DTPF1
Number of atoms included #LASTProtein: 20580 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 20580

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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)

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