1ROA | pdb_00001roa

Structure of human cystatin D

• PDB DOI: https://doi.org/10.2210/pdb1ROA/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-12-01 Released: 2004-05-18 
• Deposition Author(s): Alvarez-Fernandez, M., Liang, Y.H., Abrahamson, M., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.278 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human cystatin D, a cysteine peptidase inhibitor with restricted inhibition profile.

Alvarez-Fernandez, M., Liang, Y.H., Abrahamson, M., Su, X.D.

(2005) J Biological Chem 280: 18221-18228

• PubMed: 15728581 
• DOI: https://doi.org/10.1074/jbc.M411914200
• Primary Citation Related Structures: 
  1RN7, 1ROA


• PubMed Abstract: 
  

  Cystatins are natural inhibitors of papain-like (family C1) and legumain-related (family C13) cysteine peptidases. Cystatin D is a type 2 cystatin, a secreted inhibitor found in human saliva and tear fluid. Compared with its homologues, cystatin D presents an unusual inhibition profile with a preferential inhibition cathepsin S > cathepsin H > cathepsin L and no inhibition of cathepsin B or pig legumain. To elucidate the structural reasons for this specificity, we have crystallized recombinant human Arg(26)-cystatin D and solved its structures at room temperature and at cryo conditions to 2.5- and 1.8-A resolution, respectively. Human cystatin D presents the typical cystatin fold, with a five-stranded anti-parallel beta-sheet wrapped around a five-turn alpha-helix. The structures reveal differences in the peptidase-interacting regions when compared with other cystatins, providing plausible explanations for the restricted inhibitory specificity of cystatin D for some papain-like peptidases and its lack of reactivity toward legumain-related enzymes.

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Organizational Affiliation: 
• Department of Clinical Chemistry, Institute of Laboratory Medicine, Lund University, SE-221 85 Lund, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.93 kDa 
• Atom Count: 993 
• Modeled Residue Count: 111 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystatin D	A	122	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P28325 (Homo sapiens) Explore P28325  Go to UniProtKB:  P28325
PHAROS:  P28325 GTEx:  ENSG00000170367

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.278 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.05	α = 90
b = 81.72	β = 90
c = 46.74	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Alvarez-Fernandez, M., Liang, Y.H., Abrahamson, M., Su, X.D.

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.6: 2024-10-30
  Changes: Structure summary