[English] 日本語
Yorodumi
- EMDB-3442: Cryo-EM reconstructions of clathrin D6 cages -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3442
TitleCryo-EM reconstructions of clathrin D6 cages
Map dataCryo-EM reconstructions of clathrin D6 cages
Sample
  • Sample: Clathrin D6 Coat
  • Protein or peptide: Mouse AP180 residues 305-901
  • Protein or peptide: Bovine Auxilin residues 547-910
  • Protein or peptide: Rat Clathrin Light Chain A1: residues 1-248
  • Protein or peptide: Rat Clathrin Heavy Chain 1: residues 1-1675
KeywordsClatrhin coats / Hsc70 / auxilin / ATP / disassembly / self-association / entropic pulling
Function / homology
Function and homology information


: / : / extrinsic component of endosome membrane / presynaptic endosome / positive regulation of clathrin coat assembly / postsynaptic endocytic zone cytoplasmic component / regulation of clathrin coat assembly / presynaptic endocytic zone / RHOU GTPase cycle / RHOV GTPase cycle ...: / : / extrinsic component of endosome membrane / presynaptic endosome / positive regulation of clathrin coat assembly / postsynaptic endocytic zone cytoplasmic component / regulation of clathrin coat assembly / presynaptic endocytic zone / RHOU GTPase cycle / RHOV GTPase cycle / postsynaptic endocytic zone / clathrin vesicle coat / regulation of clathrin-dependent endocytosis / 1-phosphatidylinositol binding / synaptic vesicle budding from presynaptic endocytic zone membrane / clathrin coat of trans-Golgi network vesicle / Gap junction degradation / Formation of annular gap junctions / cell cycle / presynaptic endocytic zone membrane / Myb complex / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / clathrin light chain binding / Retrograde neurotrophin signalling / synaptic vesicle recycling / VLDLR internalisation and degradation / clathrin complex / regulation of protein transport / negative regulation of hyaluronan biosynthetic process / WNT5A-dependent internalization of FZD4 / clathrin coat / Lysosome Vesicle Biogenesis / extrinsic component of presynaptic endocytic zone membrane / Golgi Associated Vesicle Biogenesis / transferrin transport / MHC class II antigen presentation / amyloid-beta clearance by transcytosis / clathrin heavy chain binding / clathrin coat of coated pit / AP-2 adaptor complex / synaptic vesicle uncoating / extrinsic component of synaptic vesicle membrane / Recycling pathway of L1 / mitotic spindle microtubule / clathrin coat disassembly / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / inositol hexakisphosphate binding / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / photoreceptor ribbon synapse / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / membrane coat / vesicle budding from membrane / clathrin-dependent endocytosis / neurotransmitter secretion / retrograde transport, endosome to Golgi / parallel fiber to Purkinje cell synapse / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / regulation of synaptic vesicle endocytosis / ankyrin binding / positive regulation of axonogenesis / clathrin binding / establishment or maintenance of cell polarity / ubiquitin-specific protease binding / Golgi organization / phospholipase binding / regulation of endocytosis / synaptic vesicle endocytosis / mitotic spindle assembly / neuron development / intracellular transport / negative regulation of protein localization to plasma membrane / protein serine/threonine kinase binding / clathrin-coated pit / presynaptic active zone membrane / phosphatidylinositol-4,5-bisphosphate binding / axon terminus / regulation of mitotic spindle organization / heat shock protein binding / T-tubule / SH2 domain binding / axonogenesis / receptor-mediated endocytosis / SNARE binding / protein tyrosine phosphatase activity / intracellular protein transport / peptide binding / clathrin-coated endocytic vesicle membrane / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization
Similarity search - Function
Clathrin coat assembly protein AP180 / ANTH domain superfamily / Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. ...Clathrin coat assembly protein AP180 / ANTH domain superfamily / Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / AP180 N-terminal homology (ANTH) domain / ANTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / 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 / ENTH domain / 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. / ENTH/VHS / 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 light chain A / Clathrin heavy chain 1 / Auxilin / Clathrin coat assembly protein AP180
Similarity search - Component
Biological speciesMus musculus (house mouse) / Bos taurus (cattle) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsSousa R / Liao H-S / Cuellar J / Valpuesta JM / Jin AJ / Lafer EM
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Clathrin-coat disassembly illuminates the mechanisms of Hsp70 force generation.
Authors: Rui Sousa / Hsien-Shun Liao / Jorge Cuéllar / Suping Jin / José M Valpuesta / Albert J Jin / Eileen M Lafer /
Abstract: Hsp70s use ATP hydrolysis to disrupt protein-protein associations and to move macromolecules. One example is the Hsc70- mediated disassembly of the clathrin coats that form on vesicles during ...Hsp70s use ATP hydrolysis to disrupt protein-protein associations and to move macromolecules. One example is the Hsc70- mediated disassembly of the clathrin coats that form on vesicles during endocytosis. Here, we exploited the exceptional features of these coats to test three models-Brownian ratchet, power-stroke and entropic pulling-proposed to explain how Hsp70s transform their substrates. Our data rule out the ratchet and power-stroke models and instead support a collision-pressure mechanism whereby collisions between clathrin-coat walls and Hsc70s drive coats apart. Collision pressure is the complement to the pulling force described in the entropic pulling model. We also found that self-association augments collision pressure, thereby allowing disassembly of clathrin lattices that have been predicted to be resistant to disassembly. These results illuminate how Hsp70s generate the forces that transform their substrates.
History
DepositionJun 20, 2016-
Header (metadata) releaseJul 27, 2016-
Map releaseJul 27, 2016-
UpdateAug 3, 2016-
Current statusAug 3, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

3442_imageCl...

Downloads & links

-
Map

FileDownload / File: emd_3442.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstructions of clathrin D6 cages
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.65 Å/pix.
x 320 pix.
= 1168. Å		3.65 Å/pix.
x 320 pix.
= 1168. Å		3.65 Å/pix.
x 320 pix.
= 1168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-1.43189907 - 13.58245754
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 1168.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.653.653.65
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1168.0001168.0001168.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.43213.582-0.000

-
Supplemental data

-
Sample components

-
Entire : Clathrin D6 Coat

EntireName: Clathrin D6 Coat
Components
  • Sample: Clathrin D6 Coat
  • Protein or peptide: Mouse AP180 residues 305-901
  • Protein or peptide: Bovine Auxilin residues 547-910
  • Protein or peptide: Rat Clathrin Light Chain A1: residues 1-248
  • Protein or peptide: Rat Clathrin Heavy Chain 1: residues 1-1675

-
Supramolecule #1000: Clathrin D6 Coat

SupramoleculeName: Clathrin D6 Coat / type: sample / ID: 1000 / Oligomeric state: 36 triskelia / Number unique components: 4
Molecular weightTheoretical: 31.5 MDa

-
Macromolecule #1: Mouse AP180 residues 305-901

MacromoleculeName: Mouse AP180 residues 305-901 / type: protein_or_peptide / ID: 1 / Details: GST tag at N-terminus. / Number of copies: 36 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse
Molecular weightExperimental: 84.268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
SequenceUniProtKB: Clathrin coat assembly protein AP180

-
Macromolecule #2: Bovine Auxilin residues 547-910

MacromoleculeName: Bovine Auxilin residues 547-910 / type: protein_or_peptide / ID: 2 / Number of copies: 108 / Recombinant expression: Yes
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow
Molecular weightExperimental: 38.935 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
SequenceUniProtKB: Auxilin

-
Macromolecule #3: Rat Clathrin Light Chain A1: residues 1-248

MacromoleculeName: Rat Clathrin Light Chain A1: residues 1-248 / type: protein_or_peptide / ID: 3 / Name.synonym: CLC, CLCA, CLCA1 / Number of copies: 108 / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat
Molecular weightExperimental: 26.979 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
SequenceUniProtKB: Clathrin light chain A

-
Macromolecule #4: Rat Clathrin Heavy Chain 1: residues 1-1675

MacromoleculeName: Rat Clathrin Heavy Chain 1: residues 1-1675 / type: protein_or_peptide / ID: 4 / Name.synonym: CHC, CHC1 / Details: His tag at the N-terminus / Number of copies: 108 / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat
Molecular weightExperimental: 196.358 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21
SequenceUniProtKB: Clathrin heavy chain 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
Details: 20 mM MES, 2 mM MgCl2, 25 mM KCl, 10 mM (NH4)2SO4 and 2 mM DTT
GridDetails: Cu/Rh 300 mesh Quantifoil R 1.2/1.3 um grids with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 98 K / Instrument: LEICA EM CPC / Method: Blot for 1 second before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 98 K / Average: 94 K
DateJun 2, 2015
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 14.6 µm / Number real images: 450 / Average electron dose: 22 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 41000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsManual picking
CTF correctionDetails: cctffind3
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: XMIPP, Relion / Number images used: 3468
Final two d classificationNumber classes: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more