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- EMDB-8886: Cryo-EM structure of F-actin complexed with the beta-III-spectrin... -

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Entry
Database: EMDB / ID: 8886
TitleCryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain
Map dataCryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain
SampleF-actin complexed with the spectrin actin-binding domain:
Actin, cytoplasmic 1 / Spectrin beta chain, non-erythrocytic 2
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 / positive regulation of gene expression, epigenetic / kinesin binding / actin filament capping / cell junction assembly / nitric-oxide synthase binding / 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 / Ras guanyl-nucleotide exchange factor activity / Fc-gamma receptor signaling pathway involved in phagocytosis / actin binding / 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
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 7 Å resolution
AuthorsWang F / Orlova A
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 ReportPDB-ID: 6anu

SummaryFull reportAbout validation report
DateDeposition: Aug 14, 2017 / Header (metadata) release: Sep 6, 2017 / Map release: Nov 22, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.95
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.95
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6anu
  • Surface level: 0.95
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6anu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8886.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.05 Å/pix.
= 210. Å
200 pix
1.05 Å/pix.
= 210. Å
200 pix
1.05 Å/pix.
= 210. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.95 (by author), 0.95 (movie #1):
Minimum - Maximum-0.6216059 - 2.428842
Average (Standard dev.)0.12115186 (0.32677585)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 209.99998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z210.000210.000210.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.6222.4290.121

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Supplemental data

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Sample components

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Entire F-actin complexed with the spectrin actin-binding domain

EntireName: F-actin complexed with the spectrin actin-binding domain
Number of components: 3

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Component #1: protein, F-actin complexed with the spectrin actin-binding domain

ProteinName: F-actin complexed with the spectrin actin-binding domain
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Actin, cytoplasmic 1

ProteinName: Actin, cytoplasmic 1 / Recombinant expression: No
MassTheoretical: 41.78266 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Spectrin beta chain, non-erythrocytic 2

ProteinName: Spectrin beta chain, non-erythrocytic 2 / Recombinant expression: No
MassTheoretical: 32.857141 kDa
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 27.25 Å / Delta phi: -166.87 deg.
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionDetails: 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).

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 7 Å / Resolution method: OTHER / Details: model-map FSC 0.38 cut-off

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Atomic model buiding

Output model

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