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

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Basic information

Entry
Database: PDB / ID: 6anu
TitleCryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain
Components
  • Actin, cytoplasmic 1
  • Spectrin beta chain, non-erythrocytic 2
KeywordsSTRUCTURAL PROTEIN / actin binding protein / filament
Function / homologyVEGFA-VEGFR2 Pathway / RHO GTPases Activate WASPs and WAVEs / Actins signature 2. / Actins signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain signature 1. / RHO GTPases Activate Formins / Spectrin repeat / Calponin homology (CH) domain / Actin ...VEGFA-VEGFR2 Pathway / RHO GTPases Activate WASPs and WAVEs / Actins signature 2. / Actins signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain signature 1. / RHO GTPases Activate Formins / Spectrin repeat / Calponin homology (CH) domain / Actin / CH domain superfamily / Actin/actin-like conserved site / RHO GTPases activate IQGAPs / Actins and actin-related proteins signature. / Spectrin/alpha-actinin / Spectrin, beta subunit / PH-like domain superfamily / Actin, conserved site / Interaction between L1 and Ankyrins / Actin family / Spectrin repeat / Pleckstrin homology domain / B-WICH complex positively regulates rRNA expression / Calponin homology domain / Cell-extracellular matrix interactions / RAF/MAP kinase cascade / MAP2K and MAPK activation / Actinin-type actin-binding domain, conserved site / Prefoldin mediated transfer of substrate to CCT/TriC / Recycling pathway of L1 / Adherens junctions interactions / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Factors involved in megakaryocyte development and platelet production / Folding of actin by CCT/TriC / Clathrin-mediated endocytosis / COPI-mediated anterograde transport / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling by BRAF and RAF fusions / Signaling by RAS mutants / Signaling by high-kinase activity BRAF mutants / Signaling by moderate kinase activity BRAF mutants / NCAM signaling for neurite out-growth / HATs acetylate histones / MHC class II antigen presentation / Regulation of actin dynamics for phagocytic cup formation / Formation of annular gap junctions / DNA Damage Recognition in GG-NER / Gap junction degradation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / UCH proteinases / Calponin homology (CH) domain profile. / PH domain profile. / Pleckstrin homology domain, spectrin-type / cerebellar Purkinje cell layer morphogenesis / postsynaptic actin cytoskeleton organization / structural constituent of postsynaptic actin cytoskeleton / cellular response to cytochalasin B / spectrin / Tat protein binding / dense body / adult behavior / ATP-dependent chromatin remodeling / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / positive regulation of gene expression, epigenetic / kinesin binding / actin filament capping / cell junction assembly / synapse assembly / cell motility / vesicle-mediated transport / substantia nigra development / antigen processing and presentation of exogenous peptide antigen via MHC class II / cytoplasmic ribonucleoprotein granule / structural constituent of cytoskeleton / ribonucleoprotein complex / platelet aggregation / phospholipid binding / multicellular organism growth / ephrin receptor signaling pathway / negative regulation of protein binding / actin cytoskeleton / axon guidance / actin binding / Ras guanyl-nucleotide exchange factor activity / Fc-gamma receptor signaling pathway involved in phagocytosis / membrane organization / retina homeostasis / apical plasma membrane / ER to Golgi vesicle-mediated transport / vesicle / cytoskeleton / nuclear chromatin / cadherin binding / MAPK cascade / cell junction / protein deubiquitination / blood microparticle / neuronal cell body
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / cryo EM / 7 Å resolution
AuthorsWang, F. / Orlova, A. / Avery, A.W. / Hays, T.S. / Egelman, E.H.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for high-affinity actin binding revealed by a β-III-spectrin SCA5 missense mutation.
Authors: 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


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)36340
ΔGint (kcal/M)-117
Surface area (Å2)108660
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 20 / Rise per n subunits: 27.25 Å / Rotation per n subunits: -166.87 deg.
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: Protein/peptide
Actin, cytoplasmic 1 / / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 6 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Escherichia coli (E. coli) / References: UniProt: P60709
#2: Protein/peptide
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) / Gene: SPTBN2, KIAA0302, SCA5 / Production host: Escherichia coli (E. coli) / References: UniProt: O15020

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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: F-actin complexed with the spectrin actin-binding domain
Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. 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 FIELDBright-field microscopy
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
IDNameCategory
1EMAN2particle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7Rosettamodel fitting
9SPIDERinitial Euler assignment
10SPIDERfinal Euler assignment
12SPIDER3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
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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