[English] 日本語
Yorodumi
- PDB-3dtp: Tarantula heavy meromyosin obtained by flexible docking to Tarant... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3dtp
TitleTarantula heavy meromyosin obtained by flexible docking to Tarantula muscle thick filament Cryo-EM 3D-MAP
Components
  • (Myosin 2 heavy chain chimera of smooth and cardiac muscle) x 2
  • Myosin regulatory light chain
  • Smooth muscle myosin essential light chain
KeywordsCONTRACTILE PROTEIN / MUSCLE PROTEIN / SMOOTH MUSCLE / MYOSIN SUBFRAGMENT 2 / HEAVY MEROMYOSIN / ESSENTIAL LIGHT CHAIN / REGULATORY LIGHT CHAIN / MOTOR PROTEIN / COILED-COIL
Function/homologymyosin II filament / regulation of slow-twitch skeletal muscle fiber contraction / myosin light chain binding / myofibril assembly / RHO GTPases activate PAKs / regulation of the force of skeletal muscle contraction / elastic fiber assembly / adult heart development / Smooth Muscle Contraction / actomyosin structure organization ...myosin II filament / regulation of slow-twitch skeletal muscle fiber contraction / myosin light chain binding / myofibril assembly / RHO GTPases activate PAKs / regulation of the force of skeletal muscle contraction / elastic fiber assembly / adult heart development / Smooth Muscle Contraction / actomyosin structure organization / skeletal muscle myosin thick filament assembly / regulation of the force of heart contraction / myosin II complex / transition between fast and slow fiber / myosin II binding / muscle myosin complex / cardiac muscle fiber development / actin-dependent ATPase activity / myosin filament / EF-hand domain / Myosin, N-terminal, SH3-like / Myosin tail / microfilament motor activity / skeletal muscle contraction / Myosin tail / cardiac muscle hypertrophy in response to stress / actomyosin / muscle filament sliding / smooth muscle contraction / Myosin N-terminal SH3-like domain profile. / myosin complex / myofibril / structural constituent of muscle / myosin heavy chain binding / Myosin S1 fragment, N-terminal / Myosin N-terminal SH3-like domain / ATP metabolic process / Myosin motor domain profile. / Myosin head, motor domain / IQ motif profile. / IQ motif, EF-hand binding site / ventricular cardiac muscle tissue morphogenesis / cardiac muscle contraction / Myosin head (motor domain) / sarcomere / stress fiber / ADP binding / striated muscle contraction / EF-hand domain pair / Translocation of GLUT4 to the plasma membrane / regulation of heart rate / Kinesin motor domain superfamily / muscle contraction / Z disc / actin filament binding / actin binding / EF-hand calcium-binding domain profile. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain / EF-hand domain pair / ATPase activity / calmodulin binding / magnesium ion binding / protein heterodimerization activity / calcium ion binding / P-loop containing nucleoside triphosphate hydrolase / ATP binding / cytosol / Myosin II regulatory light chain / Myosin light polypeptide 6 / Myosin-11 / Myosin-7
Function and homology information
Specimen sourceGallus gallus / Chicken / bird /
Homo sapiens / / human
Avicularia avicularia / / arthropod
MethodElectron microscopy (20 Å resolution / Filament / Helical) / Transmission electron microscopy
AuthorsAlamo, L. / Wriggers, W. / Pinto, A. / Bartoli, F. / Salazar, L. / Zhao, F.Q. / Craig, R. / Padron, R.
CitationJournal: Cell / Year: 1999
Title: Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head.
Authors: A Houdusse / V N Kalabokis / D Himmel / A G Szent-Györgyi / C Cohen
Abstract: The crystal structure of a proteolytic subfragment from scallop striated muscle myosin, complexed with MgADP, has been solved at 2.5 A resolution and reveals an unusual conformation of the myosin ...The crystal structure of a proteolytic subfragment from scallop striated muscle myosin, complexed with MgADP, has been solved at 2.5 A resolution and reveals an unusual conformation of the myosin head. The converter and the lever arm are in very different positions from those in either the pre-power stroke or near-rigor state structures; moreover, in contrast to these structures, the SH1 helix is seen to be unwound. Here we compare the overall organization of the myosin head in these three states and show how the conformation of three flexible "joints" produces rearrangements of the four major subdomains in the myosin head with different bound nucleotides. We believe that this novel structure represents one of the prehydrolysis ("ATP") states of the contractile cycle in which the myosin heads stay detached from actin.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 15, 2008 / Release: Oct 7, 2008
RevisionDateData content typeGroupProviderType
1.0Oct 7, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 22, 2015Structure modelSource and taxonomy
1.3Dec 14, 2016Structure modelOther

-
Structure visualization

Movie
  • Biological unit as representative helical assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links

-
Assembly

Deposited unit
A: Myosin 2 heavy chain chimera of smooth and cardiac muscle
B: Myosin 2 heavy chain chimera of smooth and cardiac muscle
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)301,0676
Polyers301,0676
Non-polymers00
Water0
1
A: Myosin 2 heavy chain chimera of smooth and cardiac muscle
B: Myosin 2 heavy chain chimera of smooth and cardiac muscle
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 36


Theoretical massNumber of molelcules
Total (without water)10,838,410216
Polyers10,838,410216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation36
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
Helical symmetryCircular symmetry: 4 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 36 / Rise per n subunits: 145 Å / Rotation per n subunits: 3 deg.

-
Components

#1: Protein/peptide Myosin 2 heavy chain chimera of smooth and cardiac muscle / Myosin heavy chain / gizzard smooth muscle / cardiac muscle beta isoform / MyHC-beta / Myosin heavy chain slow isoform / MyHC-slow


Mass: 111851.070 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-972)
Source: (gene. exp.) Gallus gallus, homo sapiens / bird / image: Gallus gallus
Plasmid name: PVL1392, PET / Cell line (production host): SF9
Production host: Spodoptera frugiperda, Escherichia coli BL21
Strain (production host): BL21 / References: UniProt:P10587, UniProt:P12883
#2: Protein/peptide Myosin 2 heavy chain chimera of smooth and cardiac muscle / Myosin heavy chain / gizzard smooth muscle / cardiac muscle beta isoform / MyHC-beta / Myosin heavy chain slow isoform / MyHC-slow


Mass: 112051.328 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT 1(S1), DELTA-S2 (residues 2-974)
Source: (gene. exp.) Gallus gallus, homo sapiens / bird / image: Gallus gallus
Plasmid name: PVL1392, PET / Cell line (production host): SF9
Production host: Spodoptera frugiperda, Escherichia coli BL21
Strain (production host): BL21 / References: UniProt:P10587, UniProt:P12883
#3: Protein/peptide Smooth muscle myosin essential light chain / ELC / Myosin light chain alkali smooth-muscle/non-muscle isoforms / G2 catalytic / LC17-GI / LC17-NM


Mass: 16873.025 Da / Num. of mol.: 2 / Source: (gene. exp.) Gallus gallus / Chicken / bird / / Plasmid name: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda / References: UniProt:P02607
#4: Protein/peptide Myosin regulatory light chain / RLC


Mass: 21709.250 Da / Num. of mol.: 2 / Source: (natural) Avicularia avicularia / / arthropod / Tissue: leg muscle / References: UniProt:B4XT43*PLUS
Sequence detailsTHE CONFLICT LISTED FOR CHAINS A AND B, RESIDUE 2 ARE CONSISTENT WITH PDB ENTRY 1BR1 AND 1I84. THE ...THE CONFLICT LISTED FOR CHAINS A AND B, RESIDUE 2 ARE CONSISTENT WITH PDB ENTRY 1BR1 AND 1I84. THE SEQUENCE OF THE HEAVY CHAIN (CHICKEN) STRUCTURE REPORTED HERE DIFFERS FROM THAT REPORTED IN THE SWISS-PROT DATABASE (ID: P10587), THAT RESIDUE SER 2 WAS CHANGED BY ALA AND DECLARED AS CLONING ARTIFACT IN PDB 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 CHAIN A,B: 1, 205-210, 452-457, 635-655, 853-1185 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 CHAIN C,D: 1-2

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Myosin thick filaments from Tarantula striated muscle / Type: COMPLEX
Details: Polymer of a multiple myosin assembled over a paramyosin core. MODEL BUILDING: the atomic model consists of two s1 heads and a segment of s2. each heavy meromyosin consists of a chimera built by chicken smooth muscle heavy chain (1i84) for s1 plus human cardiac muscle (2fxm) for s2 (chains a,b) and two light chains, the chicken smooth muscle (1i84) for elc (chains c,d) and a homology model based on 1br1 of the tarantula skeletal muscle rlc sequence (chains e,f), this model was flexible fitted to a tarantula 3d map (emd-1535)
Buffer solutionName: 100mM NaCl, 3mM MgCl2, 1mM EGTA, 5mM PIPES, 5mM NaH2PO4, 1mM NaN3
Details: 100mM NaCl, 3mM MgCl2, 1mM EGTA, 5mM PIPES, 5mM NaH2PO4, 1mM NaN3
pH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Holey carbon grids, 400 mesh
VitrificationDetails: Plunging in a liquid ethane. 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 / Date: Sep 19, 2001
Details: Holey carbon grids Cryo preserved 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 / Cs: 2 mm
Specimen holderTemperature: 88 kelvins
Image scansNumber digital images: 465

-
Processing

EM software
IDNameVersionCategory
1Situs3.2MODEL FITTING
2X-PLOR3.851MODEL FITTING
CTF correctionDetails: no corrected
3D reconstructionMethod: Single particle reconstruction with a modification of the IHRSR method
Resolution: 20 Å / Number of particles: 15504 / Nominal pixel size: 2.48 / Actual pixel size: 2.48 / Magnification calibration: Tropomyosin paracrystal
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 were 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. 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. as an initial reference model we used the tarantula negatively stained 3d-map, which was axially rotated, axially shifted and also out of plane tilted up to plus-minus12deg. for projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus 12 deg. every 2 deg., 45 reference rotated projections (0-90 deg., every 2 deg. 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.
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--Flexible Fitting REFINEMENT PROTOCOL--Custom skeleton of 31 positional markers
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Constrained Molecular Dynamics
Atomic model building
IDPDB-ID 3D fitting ID
11I84

1i84

1
22FXM

2fxm

1
31B7T

1b7t

1
Number of atoms included #LASTProtein: 20580 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 20580

+
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 / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more