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- EMDB-39905: RAT skeletal muscle ATM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39905
TitleRAT skeletal muscle ATM complex
Map dataEM map
Sample
  • Complex: RAT skeletal muscle ATM complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Myosin heavy chain 4
    • Protein or peptide: Tropomyosin beta chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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 / actin filament / filopodium / 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 / cell body / actin binding / 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
Uncharacterized protein / Tropomyosin beta chain / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodhelical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLi DN / Zhao QY / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure Rat skeletal muscle ATM complex
Authors: Li DN / Zhao QY / Liu C
History
DepositionApr 26, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39905.png

Downloads & links

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Map

FileDownload / File: emd_39905.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0058847317 - 0.028424663
Average (Standard dev.)0.00020686004 (±0.0010980682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map

Fileemd_39905_half_map_1.map
AnnotationEM half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map

Fileemd_39905_half_map_2.map
AnnotationEM half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RAT skeletal muscle ATM complex

EntireName: RAT skeletal muscle ATM complex
Components
  • Complex: RAT skeletal muscle ATM complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Myosin heavy chain 4
    • Protein or peptide: Tropomyosin beta chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: RAT skeletal muscle ATM complex

SupramoleculeName: RAT skeletal muscle ATM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 41.374207 KDa
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIEHG IITNWDDMEK IWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV P IYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIEHG IITNWDDMEK IWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV P IYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSYEL PD GQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITALA PST MKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Tropomyosin beta chain

MacromoleculeName: Tropomyosin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 19.049244 KDa
SequenceString:
ALQKKLKGTE DEVEKYSESV KDAQEKLEQA EKKATDAEAD VASLNRRIQL VEEELDRAQE RLATALQKLE EAEKAADESE RGMKVIENR AMKDEEKMEL QEMQLKEAKH IAEDSDRKYE EVARKLVILE GELERSEERA EVAESKCGDL EEELKIVTNN L KSLEAQ

UniProtKB: Tropomyosin beta chain

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Macromolecule #3: Myosin heavy chain 4

MacromoleculeName: Myosin heavy chain 4 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 88.10857 KDa
SequenceString: MAVFGEAAPY LRKSEKERIE AQNKPFDAKS SVFVVDAKES FVKATVQSRE GGKVTAKTEG GATVTVKDDQ VFPMNPPKYD KIEDMAMMT HLHEPAVLYN LKERYAAWMI YTYSGLFCVT VNPYKWLPVY NAEVVAAYRG KKRQEAPPHI FSISDNAYQF M LTDRENQS ...String:
MAVFGEAAPY LRKSEKERIE AQNKPFDAKS SVFVVDAKES FVKATVQSRE GGKVTAKTEG GATVTVKDDQ VFPMNPPKYD KIEDMAMMT HLHEPAVLYN LKERYAAWMI YTYSGLFCVT VNPYKWLPVY NAEVVAAYRG KKRQEAPPHI FSISDNAYQF M LTDRENQS ILITGESGAG KTVNTKRVIQ YFATIAVTGE KKKEEAPSGK MQGTLEDQII SANPLLEAFG NAKTVRNDNS SR FGKFIRI HFGTTGKLAS ADIETYLLEK SRVTFQLKAE RSYHIFYQIM SNKKPDLIEM LLITTNPYDY AFVSQGEITV PSI DDQEEL MATDSAIDIL GFTSDERVSI YKLTGAVMHY GNMKFKQKQR EEQAEPDGTE VADKAAYLQN LNSADLLKAL CYPR VKVGN EYVTKGQTVQ QVYNAVGALA KAVYEKMFLW MVTRINQQLD TKQPRQYFIG VLDIAGFEIF DFNSLEQLCI NFTNE KLQQ FFNHHMFVLE QEEYKKEGIE WEFIDFGMDL AACIELIEKP MGIFSILEEE CMFPKATDTS FKNKLYEQHL GKSNNF QKP KPAKGKVEAH FSLVHYAGTV DYNIAGWLDK NKDPLNETVV GLYQKSSMKT LAYLFSGAAA AAEAESGGGG GKKGAKK KG SSFQTVSALF RENLNKLMTN LRSTHPHFVR CIIPNETKTP GAMEHELVLH QLRCNGVLEG IRICRKGFPS RILYADFK Q RYKVLNASAI PEGQFIDSKK ASEKLLGSID IDHTQYKFGH TKVFFKAGLL GLLEEMRDD

UniProtKB: Uncharacterized protein

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.69 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62956
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8efi

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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