5UYX | pdb_00005uyx

Structure of Human T-complex protein 1 subunit epsilon (CCT5)

• PDB DOI: https://doi.org/10.2210/pdb5UYX/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-24 Released: 2017-07-05 
• Deposition Author(s): Pereira, J.H., McAndrew, R.P., Sergeeva, O.A., Ralston, C.Y., King, J.A., Adams, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.318 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

Literature

Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy.

Pereira, J.H., McAndrew, R.P., Sergeeva, O.A., Ralston, C.Y., King, J.A., Adams, P.D.

(2017) Sci Rep 7: 3673-3673

• PubMed: 28623285 
• DOI: https://doi.org/10.1038/s41598-017-03825-3
• Primary Citation Related Structures: 
  5UYX, 5UYZ


• PubMed Abstract: 
  

  The human chaperonin TRiC consists of eight non-identical subunits, and its protein-folding activity is critical for cellular health. Misfolded proteins are associated with many human diseases, such as amyloid diseases, cancer, and neuropathies, making TRiC a potential therapeutic target. A detailed structural understanding of its ATP-dependent folding mechanism and substrate recognition is therefore of great importance. Of particular health-related interest is the mutation Histidine 147 to Arginine (H147R) in human TRiC subunit 5 (CCT5), which has been associated with hereditary sensory neuropathy. In this paper, we describe the crystal structures of CCT5 and the CCT5-H147R mutant, which provide important structural information for this vital protein-folding machine in humans. This first X-ray crystallographic study of a single human CCT subunit in the context of a hexadecameric complex can be expanded in the future to the other 7 subunits that form the TRiC complex.

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Organizational Affiliation: 
• Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Biology Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. [e-mail].
Department of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D8  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 240.71 kDa 
• Atom Count: 14,749 
• Modeled Residue Count: 1,901 
• Deposited Residue Count: 2,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-complex protein 1 subunit epsilon	A, B, C, D	541	Homo sapiens	Mutation(s): 0  Gene Names: CCT5, CCTE, KIAA0098 EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P48643 (Homo sapiens) Explore P48643  Go to UniProtKB:  P48643
PHAROS:  P48643 GTEx:  ENSG00000150753

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], F [auth B], G [auth C], H [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.318 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.71	α = 90
b = 204.71	β = 90
c = 162.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): Pereira, J.H., McAndrew, R.P., Sergeeva, O.A., Ralston, C.Y., King, J.A., Adams, P.D.

Revision History  

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description