[English] 日本語
Yorodumi
- PDB-4a7l: Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a7l
TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 1)
Components
  • ACTIN, ALPHA SKELETON MUSCLE
  • MYOSIN IE HEAVY CHAIN
  • TROPOMYOSIN 1 ALPHA
KeywordsSTRUCTURAL PROTEIN/HYDROLASE / STRUCTURAL PROTEIN-HYDROLASE COMPLEX / STRUCTURAL PROTEIN / CYTOSKELETON / CONTRACTILE FILAMENT / MOTOR ACTIVITY / ATP CATABOLIC PROCESS / RIGOR STATE
Function / homology
Function and homology information


macropinocytic cup membrane / pseudopodium membrane / actin wave / macropinocytic cup cytoskeleton / chemotaxis to cAMP / macropinocytic cup / actin filament-based movement / leading edge membrane / early phagosome / myosin complex ...macropinocytic cup membrane / pseudopodium membrane / actin wave / macropinocytic cup cytoskeleton / chemotaxis to cAMP / macropinocytic cup / actin filament-based movement / leading edge membrane / early phagosome / myosin complex / cytoskeletal motor activator activity / microfilament motor activity / phagocytosis, engulfment / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / cell leading edge / pseudopodium / filamentous actin / actin filament bundle / phosphatidylinositol-3,4,5-trisphosphate binding / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / phagocytic cup / skeletal muscle myofibril / actin monomer binding / phagocytosis / skeletal muscle fiber development / stress fiber / titin binding / muscle contraction / actin filament polymerization / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / calmodulin binding / hydrolase activity / protein heterodimerization activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Tropomyosins signature. / Tropomyosin / Tropomyosin / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Tropomyosins signature. / Tropomyosin / Tropomyosin / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Tropomyosin alpha-1 chain / Actin, alpha skeletal muscle / Myosin IE heavy chain
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
DICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsBehrmann, E. / Mueller, M. / Penczek, P.A. / Mannherz, H.G. / Manstein, D.J. / Raunser, S.
CitationJournal: Cell / Year: 2012
Title: Structure of the rigor actin-tropomyosin-myosin complex.
Authors: Elmar Behrmann / Mirco Müller / Pawel A Penczek / Hans Georg Mannherz / Dietmar J Manstein / Stefan Raunser /
Abstract: Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions ...Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin.
History
DepositionNov 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Derived calculations / Other / Category: cell / struct_conn / Item: _cell.Z_PDB / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1989
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1989
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACTIN, ALPHA SKELETON MUSCLE
B: TROPOMYOSIN 1 ALPHA
C: MYOSIN IE HEAVY CHAIN
D: ACTIN, ALPHA SKELETON MUSCLE
E: ACTIN, ALPHA SKELETON MUSCLE
F: ACTIN, ALPHA SKELETON MUSCLE
G: MYOSIN IE HEAVY CHAIN
H: TROPOMYOSIN 1 ALPHA
I: ACTIN, ALPHA SKELETON MUSCLE
J: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,95220
Polymers478,61510
Non-polymers2,33610
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
ACTIN, ALPHA SKELETON MUSCLE / F-ACTIN / ALPHA-ACTIN-1


Mass: 41875.633 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE / References: UniProt: P68135
#2: Protein TROPOMYOSIN 1 ALPHA


Mass: 15807.628 Da / Num. of mol.: 2 / Fragment: RESIDUES 98-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYCTOLAGUS CUNICULUS (rabbit) / Plasmid: PJC20 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P58772
#3: Protein MYOSIN IE HEAVY CHAIN / MYOE


Mass: 79207.305 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-697 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2 / Plasmid: PDXA-3H / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: Q03479, EC: 3.6.4.1
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
Compound detailsENGINEERED RESIDUE IN CHAIN C, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN G, SER 334 TO GLU ...ENGINEERED RESIDUE IN CHAIN C, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN G, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN J, SER 334 TO GLU
Sequence detailsSEQUENCE IS NOT BASED ON THE EXPERIMENTAL PROTEIN AS NO FULL-LENGTH TROPOMYOSIN STRUCTURES WERE ...SEQUENCE IS NOT BASED ON THE EXPERIMENTAL PROTEIN AS NO FULL-LENGTH TROPOMYOSIN STRUCTURES WERE AVAILABLE, BUT ON A MODEL OBTAINED FROM MD SIMULATIONS DESCRIBED IN LI, X. E. ET AL. TROPOMYOSIN POSITION ON F-ACTIN REVEALED BY EM RECONSTRUCTION AND COMPUTATIONAL CHEMISTRY. BIOPHYS J 100, 1005-1013, (2011) SEQUENCE AS DESCRIBED BY KOLLMAR, M., DURRWANG, U., KLICHE, W., MANSTEIN, D. J. & KULL, F. J. CRYSTAL STRUCTURE OF THE MOTOR DOMAIN OF A CLASS-I MYOSIN. EMBO J 21, 2517-2525, (2002).

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: F-ACTIN-MYO1E-TROPOMYOSIN COMPLEX (CONFORMATION 1) / Type: COMPLEX / Details: CMOS IMAGE FRAMES SELECTED BY POWER SPECTRUM
Buffer solutionName: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
pH: 7.2
Details: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
SpecimenConc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,

-
Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Details: BEST 836 MICROGRAPHS WERE SELECTED FROM OVER 3000 AQUIRED IMAGES
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 169644 X / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Cs: 4.1 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 1.7 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
Image scansNum. digital images: 836
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1DireXmodel fitting
2SPARX3D reconstruction
CTF correctionDetails: EACH PARTICLE
3D reconstructionMethod: IHRSR / Resolution: 8.1 Å / Num. of particles: 5555 / Nominal pixel size: 1.84 Å / Actual pixel size: 1.84 Å / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--GEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH REFINEMENT PROTOCOL--EM
Atomic model building
IDPDB-ID 3D fitting-ID
11LKX

1lkx

1
23MFP

3mfp

1
RefinementHighest resolution: 8.1 Å
Refinement stepCycle: LAST / Highest resolution: 8.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33360 0 140 0 33500

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more