5M5U

Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin.

Muenzner, J., Traub, L.M., Kelly, B.T., Graham, S.C.

(2017) Traffic 18: 44-57

  • DOI: 10.1111/tra.12457
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Short peptide motifs in unstructured regions of clathrin-adaptor proteins recruit clathrin to membranes to facilitate post-Golgi membrane transport. Three consensus clathrin-binding peptide sequences have been identified and structural studies show t ...

    Short peptide motifs in unstructured regions of clathrin-adaptor proteins recruit clathrin to membranes to facilitate post-Golgi membrane transport. Three consensus clathrin-binding peptide sequences have been identified and structural studies show that each binds distinct sites on the clathrin heavy chain N-terminal domain (NTD). A fourth binding site for adaptors on NTD has been functionally identified but not structurally characterised. We have solved high resolution structures of NTD bound to peptide motifs from the cellular clathrin adaptors β2 adaptin and amphiphysin plus a putative viral clathrin adaptor, hepatitis D virus large antigen (HDAg-L). Surprisingly, with each peptide we observe simultaneous peptide binding at multiple sites on NTD and viral peptides binding to the same sites as cellular peptides. Peptides containing clathrin-box motifs (CBMs) with the consensus sequence LΦxΦ[DE] bind at the 'arrestin box' on NTD, between β-propeller blades 4 and 5, which had previously been thought to bind a distinct consensus sequence. Further, we structurally define the fourth peptide binding site on NTD, which we term the Royle box. In vitro binding assays show that clathrin is more readily captured by cellular CBMs than by HDAg-L, and site-directed mutagenesis confirms that multiple binding sites on NTD contribute to efficient capture by CBM peptides.

    Organizational Affiliation: 

    Department of Pathology, University of Cambridge, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Clathrin heavy chain 1
A, B
365Bos taurusMutation(s): 0 
Gene Names: CLTC
Find proteins for P49951 (Bos taurus)
Go to Gene View: CLTC
Go to UniProtKB:  P49951
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Large delta antigen
E, F, G, H
9Hepatitis delta virus genotype IMutation(s): 2 
Find proteins for P0C6L6 (Hepatitis delta virus genotype I)
Go to UniProtKB:  P0C6L6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.230α = 90.00
b = 131.190β = 115.61
c = 77.870γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome Trust and Royal SocietyUnited Kingdom098406/Z/12/Z
Wellcome TrustUnited Kingdom090909/Z/09/Z
National Institutes of HealthUnited StatesGM106963

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references