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- EMDB-5119: Clathrin D6 coat -

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Basic information

Entry
Database: EMDB / ID: EMD-5119
TitleClathrin D6 coat
Map dataThis is an averaged map of clathrin D6 coat
Sample
  • Sample: Clathrin coats
  • Protein or peptide: clathrin coat
KeywordsCLATHRIN / ALPHA-ZIG-ZAG / BETA-PROPELLER / ENDOCYTOSIS/EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


postsynaptic endocytic zone cytoplasmic component / 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 ...postsynaptic endocytic zone cytoplasmic component / 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 vesicle coat / Lysosome Vesicle Biogenesis / clathrin coat of trans-Golgi network vesicle / negative regulation of hyaluronan biosynthetic process / clathrin light chain binding / clathrin complex / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin heavy chain binding / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / arrestin family protein binding / receptor-mediated endocytosis / intracellular protein transport / autophagy / synaptic vesicle membrane / spindle / disordered domain specific binding / melanosome / mitotic cell cycle / protein domain specific binding / cell division / structural molecule activity / mitochondrion / identical protein binding / plasma membrane
Similarity search - Function
Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / 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 light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / 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 / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin light chain A / Clathrin heavy chain 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsFotin A / Cheng Y / Sliz P / Grigorieff N / Harrison SC / Kirchhausen T / Walz T
CitationJournal: Nature / Year: 2004
Title: Molecular model for a complete clathrin lattice from electron cryomicroscopy.
Authors: Alexander Fotin / Yifan Cheng / Piotr Sliz / Nikolaus Grigorieff / Stephen C Harrison / Tomas Kirchhausen / Thomas Walz /
Abstract: Clathrin-coated vesicles are important vehicles of membrane traffic in cells. We report the structure of a clathrin lattice at subnanometre resolution, obtained from electron cryomicroscopy of coats ...Clathrin-coated vesicles are important vehicles of membrane traffic in cells. We report the structure of a clathrin lattice at subnanometre resolution, obtained from electron cryomicroscopy of coats assembled in vitro. We trace most of the 1,675-residue clathrin heavy chain by fitting known crystal structures of two segments, and homology models of the rest, into the electron microscopy density map. We also define the position of the central helical segment of the light chain. A helical tripod, the carboxy-terminal parts of three heavy chains, projects inward from the vertex of each three-legged clathrin triskelion, linking that vertex to 'ankles' of triskelions centred two vertices away. Analysis of coats with distinct diameters shows an invariant pattern of contacts in the neighbourhood of each vertex, with more variable interactions along the extended parts of the triskelion 'legs'. These invariant local interactions appear to stabilize the lattice, allowing assembly and uncoating to be controlled by events at a few specific sites.
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: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1xi4
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyv
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1xi4
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5119_1.tif

Downloads & links

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Map

FileDownload / File: emd_5119.map.gz / Format: CCP4 / Size: 113.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an averaged map of clathrin D6 coat
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 312 pix.
= 873.6 Å		2.8 Å/pix.
x 312 pix.
= 873.6 Å		2.8 Å/pix.
x 312 pix.
= 873.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.25 / Movie #1: 0.1
Minimum - Maximum-0.162952 - 0.637629
Average (Standard dev.)-0.00000314035 (±0.0633478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-156-156-156
Dimensions312312312
Spacing312312312
CellA=B=C: 873.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z873.600873.600873.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-156-156-156
NC/NR/NS312312312
D min/max/mean-0.1630.638-0.000

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Supplemental data

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Sample components

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Entire : Clathrin coats

EntireName: Clathrin coats
Components
  • Sample: Clathrin coats
  • Protein or peptide: clathrin coat

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Supramolecule #1000: Clathrin coats

SupramoleculeName: Clathrin coats / type: sample / ID: 1000 / Details: Clathrin coats assembled from clathrin and AP-2 / Number unique components: 9

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Macromolecule #1: clathrin coat

MacromoleculeName: clathrin coat / type: protein_or_peptide / ID: 1 / Name.synonym: clathrin coat / Number of copies: 108 / Oligomeric state: D6 assemble / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: cattle / 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: 6.5 / Details: 25mM MES pH 6.5, 2mM DTT
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: 225 / 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: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign
Details: This is an n.c.s averaged map from raw reconstruction
Number images used: 1450

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Atomic model buiding 1

Initial model(PDB ID:

1n4c

,

1bpo

,

1b89

)
SoftwareName: O
DetailsProtocol: Rigid Body. various segments of clathrin 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-1xi4:
Clathrin D6 Coat

PDB-3iyv:
Clathrin D6 coat as full-length Triskelions

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