7ZEU | pdb_00007zeu

Crystal structure of human Clusterin, crystal form II

• PDB DOI: https://doi.org/10.2210/pdb7ZEU/pdb

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


• Deposited: 2022-03-31 Released: 2023-10-11 
• Deposition Author(s): Yuste-Checa, P., Bracher, A., Hartl, F.U.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Hydrophobic tails enable diverse functions of the extracellular chaperone clusterin

Yuste-Checa, P., Carvajal, A.I., Mi, C., Paatz, S., Ulrich Hartl, F., Bracher, A.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.10.30.620894

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97.75 kDa 
• Atom Count: 5,964 
• Modelled Residue Count: 724 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clusterin	A, B [auth D]	402	Homo sapiens	Mutation(s): 0  Gene Names: CLU, APOJ, CLI, KUB1, AAG4
UniProt & NIH Common Fund Data Resources
Find proteins for P10909 (Homo sapiens) Explore P10909  Go to UniProtKB:  P10909
PHAROS:  P10909 GTEx:  ENSG00000120885
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: P10909-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D [auth C], E, F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth D], N [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.44	α = 90
b = 46.438	β = 127.2
c = 155.173	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Yuste-Checa, P., Bracher, A., Hartl, F.U.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary
• Version 1.2: 2025-04-23
  Changes: Database references