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

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Basic information

Entry
Database: PDB / ID: 3iyv
TitleClathrin D6 coat as full-length Triskelions
Components
  • Clathrin heavy chain
  • Clathrin light chain A
KeywordsEndocytosis/exocytosis / CLATHRIN / 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 / clathrin vesicle coat ...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 / clathrin vesicle coat / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin complex / negative regulation of hyaluronan biosynthetic process / clathrin light chain binding / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin coat of coated pit / clathrin heavy chain binding / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / arrestin family protein binding / receptor-mediated endocytosis / intracellular protein transport / autophagy / spindle / synaptic vesicle membrane / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsJohnson, G.T. / Fotin, A. / Cheng, Y. / Sliz, P. / Grigorieff, N. / Harrison, S.C. / Kirchhausen, T. / Walz, T.
Citation
Journal: 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.
#1: Journal: 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 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete point assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clathrin heavy chain
J: Clathrin light chain A
B: Clathrin heavy chain
K: Clathrin light chain A
C: Clathrin heavy chain
L: Clathrin light chain A
D: Clathrin heavy chain
M: Clathrin light chain A
E: Clathrin heavy chain
N: Clathrin light chain A
F: Clathrin heavy chain
O: Clathrin light chain A
G: Clathrin heavy chain
P: Clathrin light chain A
H: Clathrin heavy chain
Q: Clathrin light chain A
I: Clathrin heavy chain
R: Clathrin light chain A


Theoretical massNumber of molelcules
Total (without water)1,761,16018
Polymers1,761,16018
Non-polymers00
Water00
1
A: Clathrin heavy chain
J: Clathrin light chain A
B: Clathrin heavy chain
K: Clathrin light chain A
C: Clathrin heavy chain
L: Clathrin light chain A
D: Clathrin heavy chain
M: Clathrin light chain A
E: Clathrin heavy chain
N: Clathrin light chain A
F: Clathrin heavy chain
O: Clathrin light chain A
G: Clathrin heavy chain
P: Clathrin light chain A
H: Clathrin heavy chain
Q: Clathrin light chain A
I: Clathrin heavy chain
R: Clathrin light chain A
x 12


Theoretical massNumber of molelcules
Total (without water)21,133,920216
Polymers21,133,920216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D6 (2x6 fold dihedral))

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Components

#1: Antibody
Clathrin heavy chain / Coordinate model: Cα atoms only


Mass: 187145.125 Da / Num. of mol.: 9 / Fragment: UNP residues 1-1630 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P49951
#2: Protein
Clathrin light chain A / Lca / Coordinate model: Cα atoms only


Mass: 8539.323 Da / Num. of mol.: 9 / Fragment: UNP residues 95-164 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P04973

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CLATHRIN D6 COATS / Type: COMPLEX / Details: COATS ASSEMBLED WITH AP-2 WITH OR WITHOUT LIGHT
Buffer solutionName: 25MM MES / pH: 6.5 / Details: 25MM MES
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: VITRIFIED

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Details: LOW DOSE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51160 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 225

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Processing

EM software
IDNameCategory
1Omodel fitting
2FREALIGN3D reconstruction
3IMAGIC3D reconstruction
CTF correctionDetails: CTFTILT, FREALIGN V.6.07
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionMethod: FOURIER SPACE RECONSTRUCTION / Resolution: 7.9 Å / Num. of particles: 1450 / Actual pixel size: 2.8 Å
Details: THE COORDINATES CONTAIN ONLY A CA TRACE. PLEASE SEE PAPER(NATURE PAPER REFERENCE) FOR FURTHER DETAILS.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: DENSITY CORRELATION / Details: METHOD--VISUAL REFINEMENT PROTOCOL--MAVE
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11BPO

1bpo

11BPO1PDBexperimental model
21B89

1b89

11B892PDBexperimental model
RefinementHighest resolution: 7.9 Å
Refinement stepCycle: LAST / Highest resolution: 7.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15300 0 0 0 15300

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