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- PDB-6sct: Cryo-EM structure of the consensus triskelion hub of the clathrin... -

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Basic information

Entry
Database: PDB / ID: 6sct
TitleCryo-EM structure of the consensus triskelion hub of the clathrin coat complex
Components
  • Clathrin heavy chain
  • Clathrin light chain
KeywordsTRANSPORT PROTEIN / clathrin / coat protein / endocytosis / trafficking
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / clathrin coat of coated pit / clathrin-coated vesicle / vesicle-mediated transport / ribosomal large subunit biogenesis / intracellular protein transport / disordered domain specific binding / nucleolus ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / clathrin coat of coated pit / clathrin-coated vesicle / vesicle-mediated transport / ribosomal large subunit biogenesis / intracellular protein transport / disordered domain specific binding / nucleolus / structural molecule activity / nucleoplasm / cytosol
Similarity search - Function
Clathrin light chain / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / : / Region in Clathrin and VPS / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link ...Clathrin light chain / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / : / Region in Clathrin and VPS / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain / Nucleolar protein 16
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.69 Å
AuthorsMorris, K.L. / Cameron, A.D. / Sessions, R. / Smith, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K003461/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N008391/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L018888/1 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly.
Authors: Kyle L Morris / Joseph R Jones / Mary Halebian / Shenping Wu / Michael Baker / Jean-Paul Armache / Amaurys Avila Ibarra / Richard B Sessions / Alexander D Cameron / Yifan Cheng / Corinne J Smith /
Abstract: Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. ...Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. We present the cryo-EM structure and molecular model of assembled porcine clathrin, providing insights into interactions that stabilize key elements of the clathrin lattice, namely, between adjacent heavy chains, at the light chain-heavy chain interface and within the trimerization domain. Furthermore, we report cryo-EM maps for five different clathrin cage architectures. Fitting structural models to three of these maps shows that their assembly requires only a limited range of triskelion leg conformations, yet inherent flexibility is required to maintain contacts. Analysis of the protein-protein interfaces shows remarkable conservation of contact sites despite architectural variation. These data reveal a universal mode of clathrin assembly that allows variable cage architecture and adaptation of coated vesicle size and shape during clathrin-mediated vesicular trafficking or endocytosis.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
SupersessionDec 18, 2019ID: 6SBZ
Revision 1.3Dec 18, 2019Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jul 9, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,877,74815
Polymers1,877,74815
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area49410 Å2
ΔGint-139 kcal/mol
Surface area243230 Å2
MethodPISA

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Components

#1: Antibody
Clathrin heavy chain


Mass: 191826.344 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CLTC / Organ: BRAIN / Organ (production host): BRAIN / Production host: Sus scrofa (pig) / References: UniProt: C0MHR2
#2: Protein
Clathrin light chain


Mass: 25218.500 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CLTB / Organ: BRAIN / Organ (production host): BRAIN / Production host: Sus scrofa (pig) / References: UniProt: F1S398
Has protein modificationN

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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 cage triskelion hub consensus structure consisting of heavy and light chains
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.54 MDa / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig) / Organ: BRAIN
Source (recombinant)Organism: Sus scrofa (pig)
Buffer solutionpH: 6.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE / Details: Ambient temperature and humidity

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 82111 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 69 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf1.06CTF correction
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
12RELION2.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12785 / Details: Manual picking
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313406 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00381768
ELECTRON MICROSCOPYf_angle_d0.725147768
ELECTRON MICROSCOPYf_dihedral_angle_d7.81733048
ELECTRON MICROSCOPYf_chiral_restr0.0376156
ELECTRON MICROSCOPYf_plane_restr0.00312045

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