7U5K | pdb_00007u5k

Cryo-EM Structure of DPYSL2

  • Classification: NEUROPEPTIDE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2022-03-02 Released: 2022-12-14 
  • Deposition Author(s): Morgan, C.E., Yu, E.W.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7U5K

This is version 1.4 of the entry. See complete history

Literature

Toward structural-omics of the bovine retinal pigment epithelium.

Morgan, C.E.Zhang, Z.Miyagi, M.Golczak, M.Yu, E.W.

(2022) Cell Rep 41: 111876-111876

  • DOI: https://doi.org/10.1016/j.celrep.2022.111876
  • Primary Citation Related Structures: 
    7U5H, 7U5I, 7U5J, 7U5K, 7U5L, 7U5M, 7U5N

  • PubMed Abstract: 

    The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.


  • Organizational Affiliation
    • Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Chemistry, Thiel College, Greenville, PA 16125, USA.

Macromolecule Content 

  • Total Structure Weight: 249.4 kDa 
  • Atom Count: 15,316 
  • Modeled Residue Count: 1,972 
  • Deposited Residue Count: 2,288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydropyrimidinase-related protein 2
A, B, C, D
572Bos taurusMutation(s): 0 
UniProt
Find proteins for O02675 (Bos taurus)
Explore O02675 
Go to UniProtKB:  O02675
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO02675
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARCv3

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-01-11
    Changes: Database references
  • Version 1.3: 2024-06-12
    Changes: Data collection
  • Version 1.4: 2025-06-04
    Changes: Data collection, Structure summary