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- PDB-6bno: Structure of bare actin filament -

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Basic information

Entry
Database: PDB / ID: 6bno
TitleStructure of bare actin filament
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / Cytoskeleton / Filament
Function / homologyActin, conserved site / Actin/actin-like conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding ...Actin, conserved site / Actin/actin-like conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / troponin I binding / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle / filamentous actin / actin monomer binding / skeletal muscle fiber development / actin filament bundle assembly / skeletal muscle myofibril / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / cell body / calcium-dependent protein binding / lamellipodium / protein domain specific binding / positive regulation of gene expression / magnesium ion binding / calcium ion binding / ATP binding / identical protein binding / cytoplasm / Actin, alpha skeletal muscle
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 5.5 Å resolution
AuthorsGurel, P.S. / Alushin, G.A.
CitationJournal: Nat Nanotechnol / Year: 2018
Title: Controllable molecular motors engineered from myosin and RNA.
Authors: Tosan Omabegho / Pinar S Gurel / Clarence Y Cheng / Laura Y Kim / Paul V Ruijgrok / Rhiju Das / Gregory M Alushin / Zev Bryant
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 17, 2017 / Release: Jan 10, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 10, 2018Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,09424
Polyers332,4828
Non-polymers3,61216
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26480
ΔGint (kcal/M)-243
Surface area (Å2)122380

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Components

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


Mass: 41560.266 Da / Num. of mol.: 8 / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal Muscle / References: UniProt: P68135
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Formula: Mg / Magnesium
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: bare actin filament / Type: COMPLEX / Details: Actin filament in the ADP state / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.042 MDa / Experimental value: YES
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionDetails: Buffer was filtered through 0.44 um filter and degassed.
pH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
150 mMpotassium chlorideKCl1
21 mMmagnesium chlorideMgCl21
31 mMEGTAC14H24N2O101
410 mMimidazoleC3H4N21
52 mMTris hydrochlorideC4H11NO31
60.5 mMdithiothreitolC4H10O2S21
7200 mMadenosine triphosphateC10H16N5O13P31
80.01 %sodium azideNaN31
SpecimenConc.: 0.025 mg/ml / Details: Filamentous bare actin / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 kelvins
Details: Sample was applied to a glow-discharged holey carbon grid, incubated for 60 seconds and blotted for 3 seconds from the backside with filter paper.

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 100 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 442
Image scansSampling size: 5 microns / Width: 3838 / Height: 3710 / Movie frames/image: 24 / Used frames/image: 1-24

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Processing

EM software
IDNameVersionCategory
1Appionparticle selection
2Leginonimage acquisition
4CTFFIND3CTF correction
5FREALIGN9.11CTF correction
8DireXmodel fitting
9MDFFmodel fitting
10NAMDmodel fitting
12MDFFmodel refinement
13EMAN2initial Euler assignment
14SPARXinitial Euler assignment
15FREALIGN9.11final Euler assignment
17FREALIGN9.113D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.6 deg. / Axial rise/subunit: 28.11 Å / Axial symmetry: C1
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 63139 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingDetails: Initial models were assembled from 8 actins (3J8A) through rigid body docking in Chimera, followed by flexible fitting with DireX. Resulting models were subjected to MDFF.
Overall b value: 350 / Ref protocol: FLEXIBLE FIT / Ref space: REAL

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