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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
DescriptorActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / Cytoskeleton / Filament
Specimen sourceOryctolagus cuniculus / mammal / Rabbit / アナウサギ /
MethodElectron microscopy (5.5 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
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: 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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 8 / Formula: C10H15N5O10P2

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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 / Details: Actin filament in the ADP state / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.042 deg. / Units: MEGADALTONS / Experimental value: YES
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
8DireXMODEL FITTING1
9MDFFMODEL FITTING1
10NAMDMODEL FITTING1
12MDFFMODEL REFINEMENT1
13EMAN2INITIAL EULER ASSIGNMENT1
14SPARXINITIAL EULER ASSIGNMENT1
15FREALIGN9.11FINAL EULER ASSIGNMENT1
17FREALIGN9.11RECONSTRUCTION1
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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