Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 41.9 kDa 
• Atom Count: 2,845 
• Modelled Residue Count: 342 
• Deposited Residue Count: 368 
• Unique protein chains: 2

 7JXV

ANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia protein) bound to ubiquitin

• PDB DOI:  https://doi.org/10.2210/pdb7JXV/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-28 Released: 2021-08-04 
• Deposition Author(s): Pashkova, N., Gakhar, L., Schnicker, N.J., Piper, R.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.264 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals.

Pashkova, N., Gakhar, L., Yu, L., Schnicker, N.J., Minard, A.Y., Winistorfer, S., Johnson, I.E., Piper, R.C.

(2021) Elife 10

• PubMed: 34821552 
• DOI: https://doi.org/10.7554/eLife.72583
• Primary Citation of Related Structures:  
  7JXV


• PubMed Abstract: 
  

Attachment of ubiquitin (Ub) to cell surface proteins serves as a signal for internalization via clathrin-mediated endocytosis (CME). How ubiquitinated membrane proteins engage the internalization apparatus remains unclear. The internalization apparatus contains proteins such as Epsin and Eps15, which bind Ub, potentially acting as adaptors for Ub-based internalization signals. Here, we show that additional components of the endocytic machinery including CALM, HIP1R, and Sla2 bind Ub via their N-terminal ANTH domain, a domain belonging to the superfamily of ENTH and VHS domains. Structural studies revealed that Ub binds with µM affinity to a unique C-terminal region within the ANTH domain not found in ENTH domains. Functional studies showed that combined loss of Ub-binding by ANTH-domain proteins and other Ub-binding domains within the yeast internalization apparatus caused defects in the Ub-dependent internalization of the GPCR Ste2 that was engineered to rely exclusively on Ub as an internalization signal. In contrast, these mutations had no effect on the internalization of Ste2 engineered to use an alternate Ub-independent internalization signal. These studies define new components of the internalization machinery that work collectively with Epsin and Eps15 to specify recognition of Ub as an internalization signal.

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Organizational Affiliation: 

Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-binding clathrin assembly protein	A	292	Rattus norvegicus	Mutation(s): 0  Gene Names: Picalm, Calm
UniProt
Find proteins for O55012 (Rattus norvegicus) Explore O55012  Go to UniProtKB:  O55012

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.264 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.068	α = 90
b = 94.068	β = 90
c = 91.39	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Pashkova, N., Gakhar, L., Schnicker, N.J., Piper, R.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM058202

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references