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- PDB-6anu: Cryo-EM structure of F-actin complexed with the beta-III-spectrin... -

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Entry
Database: PDB / ID: 6anu
TitleCryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain
DescriptorActin
cytoplasmic 1
Spectrin beta chain
non-erythrocytic 2
KeywordsSTRUCTURAL PROTEIN / actin binding protein / filament
Specimen sourceHomo sapiens / human
MethodElectron microscopy (7 Å resolution / Filament / Helical)
AuthorsWang, F. / Orlova, A. / Avery, A.W. / Hays, T.S. / Egelman, E.H.
CitationNat Commun, 2017, 8, 1350-1350

Nat Commun, 2017, 8, 1350-1350 Yorodumi Papers
Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation.
Adam W Avery / Michael E Fealey / Fengbin Wang / Albina Orlova / Andrew R Thompson / David D Thomas / Thomas S Hays / Edward H Egelman

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 14, 2017 / Release: Nov 22, 2017

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Assembly

Deposited unit
F: Actin, cytoplasmic 1
A: Actin, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
f: Spectrin beta chain, non-erythrocytic 2
a: Spectrin beta chain, non-erythrocytic 2
b: Spectrin beta chain, non-erythrocytic 2
c: Spectrin beta chain, non-erythrocytic 2
d: Spectrin beta chain, non-erythrocytic 2
e: Spectrin beta chain, non-erythrocytic 2


Theoretical massNumber of molelcules
Total (without water)447,83912
Polyers447,83912
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)36340
ΔGint (kcal/M)-117
Surface area (Å2)108660
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = -166.87 DEGREES RISE PER SUBUNIT (HEIGHT) = 27.25 ANGSTROMS

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Components

#1: Polypeptide(L)
Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 6 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P60709
#2: Polypeptide(L)
Spectrin beta chain, non-erythrocytic 2 / Beta-III spectrin / Spinocerebellar ataxia 5 protein


Mass: 32857.141 Da / Num. of mol.: 6 / Mutation: L253P / Source: (gene. exp.) Homo sapiens / human / References: UniProt: O15020

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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: F-actin complexed with the spectrin actin-binding domain
Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: negative stain
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 3 sec. / Electron dose: 20 e/Å2
Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: dev_2471: / Classification: refinement
EM software
IDNameCategoryImage processing IDImaging IDFitting ID
1EMAN2PARTICLE SELECTION1
2EPUIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7RosettaMODEL FITTING1
9SPIDERINITIAL EULER ASSIGNMENT1
10SPIDERFINAL EULER ASSIGNMENT1
12SPIDERRECONSTRUCTION1
13PHENIXMODEL REFINEMENT1
14CootMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.87 deg. / Axial rise/subunit: 27.25 Å / Axial symmetry: C1
3D reconstructionResolution: 7 Å / Resolution method: OTHER / Number of particles: 12443 / Algorithm: BACK PROJECTION / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00648396
ELECTRON MICROSCOPYf_angle_d1.00387534
ELECTRON MICROSCOPYf_dihedral_angle_d7.67219314
ELECTRON MICROSCOPYf_chiral_restr0.0553714
ELECTRON MICROSCOPYf_plane_restr0.0067344

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