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- PDB-8zbm: RAT skeletal muscle ATM complex -

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Basic information

Entry
Database: PDB / ID: 8zbm
TitleRAT skeletal muscle ATM complex
Components
  • Actin, alpha skeletal muscle
  • Myosin heavy chain 4
  • Tropomyosin beta chain
KeywordsPROTEIN FIBRIL / Protein complex
Function / homology
Function and homology information


Formation of the dystrophin-glycoprotein complex (DGC) / skeletal muscle fiber adaptation / Striated Muscle Contraction / Smooth Muscle Contraction / myosin filament assembly / actomyosin contractile ring / A band / muscle myosin complex / myosin filament / cellular response to potassium ion ...Formation of the dystrophin-glycoprotein complex (DGC) / skeletal muscle fiber adaptation / Striated Muscle Contraction / Smooth Muscle Contraction / myosin filament assembly / actomyosin contractile ring / A band / muscle myosin complex / myosin filament / cellular response to potassium ion / response to steroid hormone / microfilament motor activity / response to muscle activity / myofibril / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / intercalated disc / response to mechanical stimulus / striated muscle contraction / skeletal muscle fiber development / stress fiber / muscle contraction / actin filament organization / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic ribonucleoprotein granule / actin filament binding / cell-cell junction / lamellipodium / actin cytoskeleton / actin binding / cell body / calmodulin binding / hydrolase activity / protein heterodimerization activity / positive regulation of gene expression / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / 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 / Uncharacterized protein / Tropomyosin beta chain / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLi, D.N. / Zhao, Q.Y. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure Rat skeletal muscle ATM complex
Authors: Li, D.N. / Zhao, Q.Y. / Liu, C.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
O: Actin, alpha skeletal muscle
Q: Actin, alpha skeletal muscle
C: Tropomyosin beta chain
P: Actin, alpha skeletal muscle
R: Actin, alpha skeletal muscle
A: Myosin heavy chain 4
B: Tropomyosin beta chain
D: Myosin heavy chain 4
G: Tropomyosin beta chain
F: Tropomyosin beta chain
J: Myosin heavy chain 4
L: Myosin heavy chain 4
K: Myosin heavy chain 4
N: Myosin heavy chain 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)855,65722
Polymers853,09416
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41374.207 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P68136, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
Tropomyosin beta chain / Beta-tropomyosin / Tropomyosin-2


Mass: 19049.244 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P58775
#3: Protein
Myosin heavy chain 4


Mass: 88108.570 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F1LRV9
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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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: RAT skeletal muscle ATM complex / Type: COMPLEX / Entity ID: #1, #3, #2 / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -166.69 ° / Axial rise/subunit: 27.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62956 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00559434
ELECTRON MICROSCOPYf_angle_d0.63980188
ELECTRON MICROSCOPYf_dihedral_angle_d4.04436154
ELECTRON MICROSCOPYf_chiral_restr0.0448808
ELECTRON MICROSCOPYf_plane_restr0.00410334

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