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- EMDB-5120: Clathrin D6 coat with auxilin J-domain -

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Basic information

Entry
Database: EMDB / ID: EMD-5120
TitleClathrin D6 coat with auxilin J-domain
Map dataThis is a volume of clathrin D6 coat bound with auxilin
Sample
  • Sample: CLATHRIN COATS BOUND WITH AUXILIN(547-910)
  • Protein or peptide: clathrin coat bound with Auxilin
KeywordsCLATHRIN / AUXILIN / ENDOCYTOSIS/EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


regulation of clathrin coat assembly / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle ...regulation of clathrin coat assembly / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / synaptic vesicle recycling / clathrin complex / negative regulation of hyaluronan biosynthetic process / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin heavy chain binding / clathrin coat of coated pit / synaptic vesicle uncoating / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / arrestin family protein binding / clathrin-coated vesicle / clathrin binding / intracellular transport / heat shock protein binding / receptor-mediated endocytosis / protein tyrosine phosphatase activity / intracellular protein transport / SH3 domain binding / autophagy / spindle / disordered domain specific binding / melanosome / presynapse / mitotic cell cycle / vesicle / molecular adaptor activity / postsynaptic density / protein domain specific binding / cell division / intracellular membrane-bounded organelle / structural molecule activity / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain ...Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain 1 / Auxilin
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsFotin A / Cheng Y / Sliz P / Grigorieff N / Harrison SC / Kirchhausen T / Walz T
CitationJournal: Nature / Year: 2004
Title: Structure of an auxilin-bound clathrin coat and its implications for the mechanism of uncoating.
Authors: Alexander Fotin / Yifan Cheng / Nikolaus Grigorieff / Thomas Walz / Stephen C Harrison / Tomas Kirchhausen /
Abstract: Clathrin-coated pits invaginate from specific membrane compartments and pinch off as coated vesicles. These vesicles then uncoat rapidly once released. The Hsc70 molecular chaperone effects the ...Clathrin-coated pits invaginate from specific membrane compartments and pinch off as coated vesicles. These vesicles then uncoat rapidly once released. The Hsc70 molecular chaperone effects the uncoating reaction, and is guided to appropriate locations on clathrin lattices by the J-domain-containing co-chaperone molecule auxilin. This raises the question of how a local event such as ATP hydrolysis by Hsc70 can catalyse a global disassembly. Here, we have used electron cryomicroscopy to determine 12-A-resolution structures of in-vitro-assembled clathrin coats in association with a carboxy-terminal fragment of auxilin that contains both the clathrin-binding region and the J domain. We have located the auxilin fragment by computing differences between these structures and those lacking auxilin (described in an accompanying paper). Auxilin binds within the clathrin lattice near contacts between an inward-projecting C-terminal helical tripod and the crossing of two 'ankle' segments; it also contacts the terminal domain of yet another clathrin 'leg'. It therefore recruits Hsc70 to the neighbourhood of a set of critical interactions. Auxilin binding produces a local change in heavy-chain contacts, creating a detectable global distortion of the clathrin coat. We propose a mechanism by which local destabilization of the lattice promotes general uncoating.
History
DepositionJun 8, 2009-
Header (metadata) releaseSep 30, 2009-
Map releaseSep 30, 2009-
UpdateMay 5, 2010-
Current statusMay 5, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1xi5
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1xi5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5120_1.tif

Downloads & links

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Map

FileDownload / File: emd_5120.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume of clathrin D6 coat bound with auxilin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 256 pix.
= 1075.2 Å		4.2 Å/pix.
x 256 pix.
= 1075.2 Å		4.2 Å/pix.
x 256 pix.
= 1075.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.288891 - 0.57785
Average (Standard dev.)0.011843 (±0.0758866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 1075.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1075.2001075.2001075.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.2890.5780.012

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Supplemental data

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Sample components

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Entire : CLATHRIN COATS BOUND WITH AUXILIN(547-910)

EntireName: CLATHRIN COATS BOUND WITH AUXILIN(547-910)
Components
  • Sample: CLATHRIN COATS BOUND WITH AUXILIN(547-910)
  • Protein or peptide: clathrin coat bound with Auxilin

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Supramolecule #1000: CLATHRIN COATS BOUND WITH AUXILIN(547-910)

SupramoleculeName: CLATHRIN COATS BOUND WITH AUXILIN(547-910) / type: sample / ID: 1000
Details: Clathrin coats assembled from clathrin and AP-2 with excess of Auxilin(547-910) added
Number unique components: 9

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Macromolecule #1: clathrin coat bound with Auxilin

MacromoleculeName: clathrin coat bound with Auxilin / type: protein_or_peptide / ID: 1 / Name.synonym: clathrin coat bound with Auxilin / Number of copies: 108 / Oligomeric state: D6 assemble / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: cow / Tissue: Brain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
Details: 20 mM Hepes, pH7.0, 2mM MgCl2,25mM KCl, 10mM (NH4)2SO4
GridDetails: holey carbon grid
VitrificationCryogen name: ETHANE / Chamber temperature: 93 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 93 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 190 / Od range: 1.4 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51159 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correction of each particle.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign / Number images used: 900

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Atomic model buiding 1

Initial model(PDB ID:

1n4c

,

1bpo

,

1b89

)
SoftwareName: O
DetailsProtocol: Rigid Body. various segment of clathrin heavy chain were separately fitted by manual docking using program O, and fitting was improved by MAVE
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: DENSITY CORRELATION
Output model

PDB-1xi5:
Clathrin D6 coat with auxilin J-domain

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