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- PDB-2y83: Actin filament pointed end -

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Basic information

Entry
Database: PDB / ID: 2y83
TitleActin filament pointed end
ComponentsACTIN, ALPHA SKELETAL MUSCLE
KeywordsCONTRACTILE PROTEIN / CYTOSKELETON / CELL MOTILITY
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 22.9 Å
AuthorsNarita, A. / Oda, T. / Maeda, Y.
CitationJournal: EMBO J / Year: 2011
Title: Structural basis for the slow dynamics of the actin filament pointed end.
Authors: Akihiro Narita / Toshiro Oda / Yuichiro Maéda /
Abstract: The actin filament has clear polarity where one end, the pointed end, has a much slower polymerization and depolymerization rate than the other end, the barbed end. This intrinsic difference of the ...The actin filament has clear polarity where one end, the pointed end, has a much slower polymerization and depolymerization rate than the other end, the barbed end. This intrinsic difference of the ends significantly affects all actin dynamics in the cell, which has central roles in a wide spectrum of cellular functions. The detailed mechanism underlying this difference has remained elusive, because high-resolution structures of the filament ends have not been available. Here, we present the structure of the actin filament pointed end obtained using a single particle analysis of cryo-electron micrographs. We determined that the terminal pointed end subunit is tilted towards the penultimate subunit, allowing specific and extra loop-to-loop inter-strand contacts between the two end subunits, which is not possible in other parts of the filament. These specific contacts prevent the end subunit from dissociating. For elongation, the loop-to-loop contacts also inhibit the incorporation of another actin monomer at the pointed end. These observations are likely to account for the less dynamic pointed end.
History
DepositionFeb 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other / Version format compliance
Revision 1.2Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_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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Assembly

Deposited unit
O: ACTIN, ALPHA SKELETAL MUSCLE
P: ACTIN, ALPHA SKELETAL MUSCLE
Q: ACTIN, ALPHA SKELETAL MUSCLE
R: ACTIN, ALPHA SKELETAL MUSCLE
S: ACTIN, ALPHA SKELETAL MUSCLE
T: ACTIN, ALPHA SKELETAL MUSCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,97918
Polymers251,1766
Non-polymers2,80412
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 / ALPHA-ACTIN-1


Mass: 41862.613 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE / References: UniProt: P68135
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: RABBIT SKELETAL ACTIN / Type: COMPLEX
Buffer solutionName: 50 MM NACL, 10 MM SODIUM PHOSPHATE BUFFER PH 7.4 3 MM MGCL2, 0.005% (W/V) NAN3, 0.7 MM DTT.
pH: 7.4
Details: 50 MM NACL, 10 MM SODIUM PHOSPHATE BUFFER PH 7.4 3 MM MGCL2, 0.005% (W/V) NAN3, 0.7 MM DTT.
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 - CRYOGEN- ETHANE, HUMIDITY- 90%, TEMPERATURE- 4 DEGREES CELSIUS. METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING.

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 8000 nm / Nominal defocus min: 5000 nm
Specimen holderTemperature: 4 K
Image recordingElectron dose: 34 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 142

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Processing

EM softwareName: EOS / Category: 3D reconstruction
CTF correctionDetails: PHASE AND AMPLITUDE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SINGLE PARTICLE ANALYSIS / Resolution: 22.9 Å / Num. of particles: 714 / Nominal pixel size: 3.4125 Å / Actual pixel size: 3.4125 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1872.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--RIGID BODY AND MOLECULAR DYNAMICS REFINEMENT PROTOCOL--EM
Atomic model buildingPDB-ID: 2ZWH

2zwh


Accession code: 2ZWH / Source name: PDB / Type: experimental model
RefinementHighest resolution: 22.9 Å
Refinement stepCycle: LAST / Highest resolution: 22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17598 0 168 0 17766

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