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- EMDB-6101: CryoEM reveals different coronin binding modes for ADP- and ADP-B... -

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Basic information

Entry
Database: EMDB / ID: EMD-6101
TitleCryoEM reveals different coronin binding modes for ADP- and ADP-BeFx- actin filaments
Map dataActin-coronin complex in ADP-BeFx state
Sample
  • Sample: Actin-Coronin complex in ADP-BeFx state
  • Protein or peptide: actin
  • Protein or peptide: Coronin 1
Keywordsactin / coronin
Function / homology
Function and homology information


positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch localization / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / troponin I binding / mesenchyme migration ...positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch localization / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / troponin I binding / mesenchyme migration / filamentous actin / actin filament bundle / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / skeletal muscle myofibril / actin monomer binding / microtubule-based process / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / protein-macromolecule adaptor activity / cell body / microtubule binding / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Coronin-like protein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Saccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsGe P / Durer ZAO / Kudryashov D / Zhou ZH / Reisler E
CitationJournal: Nat Struct Mol Biol / Year: 2014
Title: Cryo-EM reveals different coronin binding modes for ADP- and ADP-BeFx actin filaments.
Authors: Peng Ge / Zeynep A Oztug Durer / Dmitri Kudryashov / Z Hong Zhou / Emil Reisler /
Abstract: Essential cellular processes involving the actin cytoskeleton are regulated by auxiliary proteins that can sense the nucleotide state of actin. Here we report cryo-EM structures for ADP-bound and ADP- ...Essential cellular processes involving the actin cytoskeleton are regulated by auxiliary proteins that can sense the nucleotide state of actin. Here we report cryo-EM structures for ADP-bound and ADP-beryllium fluoride (ADP-BeFx, an ADP-Pi mimic)-bound actin filaments in complex with the β-propeller domain of yeast coronin 1 (crn1), at 8.6-Å resolution. Our structures reveal the main differences in the interaction of coronin with the two nucleotide states of F-actin. We derived pseudoatomic models by fitting the atomic structures of actin and coronin into the EM envelopes and confirmed the identified interfaces on actin by chemical cross-linking, fluorescence spectroscopy and actin mutagenesis. The models offer a structural explanation for the nucleotide-dependent effects of coronin on cofilin-assisted remodeling of F-actin.
History
DepositionSep 20, 2014-
Header (metadata) releaseOct 15, 2014-
Map releaseNov 5, 2014-
UpdateDec 10, 2014-
Current statusDec 10, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 13.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6101.gif

Downloads & links

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Map

FileDownload / File: emd_6101.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActin-coronin complex in ADP-BeFx state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 320 pix.
= 459.84 Å		1.44 Å/pix.
x 320 pix.
= 459.84 Å		1.44 Å/pix.
x 320 pix.
= 459.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.437 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.199999999999999 / Movie #1: 13.2
Minimum - Maximum-14.544685360000001 - 43.758926389999999
Average (Standard dev.)-0.01767861 (±2.45434046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 459.84003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4371.4371.437
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z459.840459.840459.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-14.54543.759-0.018

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Supplemental data

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Sample components

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Entire : Actin-Coronin complex in ADP-BeFx state

EntireName: Actin-Coronin complex in ADP-BeFx state
Components
  • Sample: Actin-Coronin complex in ADP-BeFx state
  • Protein or peptide: actin
  • Protein or peptide: Coronin 1

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Supramolecule #1000: Actin-Coronin complex in ADP-BeFx state

SupramoleculeName: Actin-Coronin complex in ADP-BeFx state / type: sample / ID: 1000
Oligomeric state: helix; one coronin subunit per one actin subunit
Number unique components: 2

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Macromolecule #1: actin

MacromoleculeName: actin / type: protein_or_peptide / ID: 1 / Oligomeric state: helix / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: muscle
Molecular weightTheoretical: 42 KDa
SequenceUniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Coronin 1

MacromoleculeName: Coronin 1 / type: protein_or_peptide / ID: 2 / Name.synonym: crn1 / Oligomeric state: helix / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 72 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 (DE3)
SequenceUniProtKB: Coronin-like protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
Details: 10 mM Tris, 0.2 mM CaCl2, 1 mM MgCl2, 50 mM KCl, 0.1 mM BeCl2, 5 mM NaF, 1 mM DTT
GridDetails: 300 Me Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK IV
Method: blot force 1, blot time 4s, blot once, wait time 2s, drain time 2s; sample volume applied to each grid was 2.5 uL

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 77 K
Alignment procedureLegacy - Astigmatism: Relion software correction
DateDec 12, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1200 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104384 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsRelion-based IHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 28.23 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: OTHER / Software - Name: Relion, IHRSR
CTF correctionDetails: Each particle

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