2CH9 | pdb_00002ch9

Crystal structure of dimeric human cystatin F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.241 (Depositor), 0.304 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2CH9

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Structural Basis of Reduction-Dependent Activation of Human Cystatin F.

Schuttelkopf, A.W.Hamilton, G.Watts, C.Van Aalten, D.M.F.

(2006) J Biological Chem 281: 16570

  • DOI: https://doi.org/10.1074/jbc.M601033200
  • Primary Citation Related Structures: 
    2CH9

  • PubMed Abstract: 

    Cystatins are important natural cysteine protease inhibitors targeting primarily papain-like cysteine proteases, including cathepsins and parasitic proteases like cruzipain, but also mammalian asparaginyl endopeptidase. Mammalian cystatin F, which is expressed almost exclusively in hematopoietic cells and accumulates in lysosome-like organelles, has been implicated in the regulation of antigen presentation and other immune processes. It is an unusual cystatin superfamily member with a redox-regulated activation mechanism and a restricted specificity profile. We describe the 2.1A crystal structure of human cystatin F in its dimeric "off" state. The two monomers interact in a fashion not seen before for cystatins or cystatin-like proteins that is crucially dependent on an unusual intermolecular disulfide bridge, suggesting how reduction leads to monomer formation and activation. Strikingly, core sugars for one of the two N-linked glycosylation sites of cystatin F are well ordered, and their conformation and interactions with the protein indicate that this unique feature of cystatin F may modulate its inhibitory properties, in particular its reduced affinity toward asparaginyl endopeptidase compared with other cystatins.


  • Organizational Affiliation
    • Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.

Macromolecule Content 

  • Total Structure Weight: 16.43 kDa 
  • Atom Count: 1,167 
  • Modeled Residue Count: 126 
  • Deposited Residue Count: 131 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYSTATIN F131Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O76096 (Homo sapiens)
Explore O76096 
Go to UniProtKB:  O76096
PHAROS:  O76096
GTEx:  ENSG00000077984 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76096
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O76096-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G28454KX
GlyCosmos: G28454KX
GlyGen: G28454KX

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
I [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.241 (Depositor), 0.304 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.345α = 90
b = 65.345β = 90
c = 123.183γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary