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- PDB-6bnu: Structure of bare actin filament, backbone-averaged with sidechai... -

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Basic information

Entry
Database: PDB / ID: 6bnu
TitleStructure of bare actin filament, backbone-averaged with sidechains truncated to alanine
DescriptorActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / Cytoskeleton / Filament
Specimen sourceOryctolagus cuniculus / mammal / Rabbit / アナウサギ /
MethodElectron microscopy (7.5 Å resolution / Filament / Helical)
AuthorsGurel, P.S. / Alushin, G.A.
CitationElife, 2017, 6

primary. Elife, 2017, 6 Yorodumi Papers
Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity.
Pinar S Gurel / Laura Y Kim / Paul V Ruijgrok / Tosan Omabegho / Zev Bryant / Gregory M Alushin

#1. Nat Nanotechnol, 2017 Yorodumi Papers
Controllable molecular motors engineered from myosin and RNA.
Omabegho, T. / Gurel, P.S. / Cheng, C.Y. / Kim, L.Y. / Ruijgrok, P.V. / Das, R. / Alushin, G.M. / Bryant, Z.

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


Theoretical massNumber of molelcules
Total (without water)332,4828
Polyers332,4828
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41560.266 Da / Num. of mol.: 8
Source: (natural) Oryctolagus cuniculus / mammal / アナウサギ /
References: UniProt: P68135

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

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Sample preparation

ComponentName: Bare actin filament / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.042 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus
Buffer solutionDetails: Buffer was filtered through 0.44 um filter and degassed.
pH: 7.5
Buffer component
IDConc.UnitsNameFormulaBuffer ID
150mMpotassium chlorideKCl1
21mMmagnesium chlorideMgCl21
31mMEGTAC14H24N2O101
410mMimidazoleC3H4N21
52mMTris hydrochlorideC4H11NO31
60.5mMdithiothreitolC4H10O2S21
7200mMadenosine 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 FIELD / 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 / Dimension width: 3838 / Dimension height: 3710 / Movie frames/image: 24 / Used frames/image: 1-24

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1AppionPARTICLE SELECTION1
2LeginonIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
5FREALIGN9.11CTF CORRECTION1
10EMAN2INITIAL EULER ASSIGNMENT1
11SPARXINITIAL EULER ASSIGNMENT1
12FREALIGN9.11FINAL EULER ASSIGNMENT1
14FREALIGN9.11RECONSTRUCTION1
15PHENIXMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.65 deg. / Axial rise/subunit: 28.11 Å / Axial symmetry: C1
3D reconstructionResolution: 7.5 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: Atomistic model was backbone-averaged in Phenix; side chains were truncated to alanine. This treatment has resulted in the errors noted in the associated caveats.
Overall b value: 350 / Ref protocol: FLEXIBLE FIT / Ref space: REAL

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