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- PDB-4a7h: Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2) -

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Basic information

Entry
Database: PDB / ID: 4a7h
TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2)
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • MYOSIN IE HEAVY CHAIN
  • TROPOMYOSIN 1-ALPHA CHAIN
KeywordsSTRUCTURAL PROTEIN/HYDROLASE / STRUCTURAL PROTEIN-HYDROLASE COMPLEX / STRUCTURAL PROTEIN / CYTOSKELETON / CONTRACTILE FILAMENT / MOTOR ACTIVITY / MYOSIN BINDING / ACTIN BINDING / 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 / phagocytosis, engulfment / myosin heavy chain binding / microfilament motor activity / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / pseudopodium / mesenchyme migration / cell leading edge / phosphatidylinositol-3,4,5-trisphosphate binding / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / phagocytosis / phagocytic cup / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / actin filament organization / filopodium / 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 / lamellipodium / actin cytoskeleton / 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 / cytoplasm / cytosol
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: 7.8 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 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1988
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Structure viewerMolecule:
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Assembly

Deposited unit
A: ACTIN, ALPHA SKELETAL MUSCLE
B: TROPOMYOSIN 1-ALPHA CHAIN
C: MYOSIN IE HEAVY CHAIN
D: ACTIN, ALPHA SKELETAL MUSCLE
E: ACTIN, ALPHA SKELETAL MUSCLE
F: ACTIN, ALPHA SKELETAL MUSCLE
G: ACTIN, ALPHA SKELETAL MUSCLE
H: TROPOMYOSIN 1-ALPHA CHAIN
I: MYOSIN IE HEAVY CHAIN
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

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Components

#1: Protein
ACTIN, ALPHA SKELETAL 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) / Organ: SARCOPLASM / Tissue: SKELETAL MUSCLE / References: UniProt: P68135
#2: Protein TROPOMYOSIN 1-ALPHA CHAIN


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) / Tissue: GIZZARD / 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 I, SER 334 TO GLU ...ENGINEERED RESIDUE IN CHAIN C, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN I, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN J, SER 334 TO GLU
Has protein modificationY
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).

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: F-ACTIN-MYO1E-TROPOMYOSIN COMPLEX (CONFORMATION 2) / 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,

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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

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Processing

EM software
IDNameCategory
1DireXmodel fitting
2SPARX3D reconstruction
CTF correctionDetails: EACH PARTICLE
3D reconstructionMethod: IHRSR / Resolution: 7.8 Å / Num. of particles: 9650 / Nominal pixel size: 1.84 Å / Actual pixel size: 1.84 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1988 (DEPOSITION ID: 10379).
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-IDAccession codeInitial refinement model-IDSource nameType
13MFP

3mfp

13MFP1PDBexperimental model
21LKX

1lkx

11LKX2PDBexperimental model
RefinementHighest resolution: 7.8 Å
Refinement stepCycle: LAST / Highest resolution: 7.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33360 0 140 0 33500

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