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- PDB-1f2r: NMR STRUCTURE OF THE HETERODIMERIC COMPLEX BETWEEN CAD DOMAINS OF... -

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Basic information

Entry
Database: PDB / ID: 1f2r
TitleNMR STRUCTURE OF THE HETERODIMERIC COMPLEX BETWEEN CAD DOMAINS OF CAD AND ICAD
Components
  • CASPASE-ACTIVATED DNASE
  • INHIBITOR OF CASPASE-ACTIVATED DNASE
KeywordsDNA BINDING PROTEIN / ALPHA-BETA ROLL / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of deoxyribonuclease activity / deoxyribonuclease inhibitor activity / Apoptosis induced DNA fragmentation / negative regulation of apoptotic DNA fragmentation / DNA nuclease activity / Hydrolases / apoptotic chromosome condensation / apoptotic DNA fragmentation / nuclease activity / negative regulation of execution phase of apoptosis ...negative regulation of deoxyribonuclease activity / deoxyribonuclease inhibitor activity / Apoptosis induced DNA fragmentation / negative regulation of apoptotic DNA fragmentation / DNA nuclease activity / Hydrolases / apoptotic chromosome condensation / apoptotic DNA fragmentation / nuclease activity / negative regulation of execution phase of apoptosis / DNA catabolic process / thymocyte apoptotic process / chaperone-mediated protein folding / protein folding chaperone / DNA endonuclease activity / disordered domain specific binding / regulation of apoptotic process / positive regulation of apoptotic process / protein domain specific binding / chromatin / nucleolus / enzyme binding / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
DNA fragmentation factor 45kDa, middle domain / DNA fragmentation factor 45 / DNA fragmentation factor 45kDa, C-terminal / DNA Fragmentation factor 45kDa, C terminal domain / DNA fragmentation factor 40, C-terminal / DNA fragmentation factor 40 / DNA fragmentation factor 40 kDa / CIDE-N domain / CIDE-N domain / CIDE-N domain profile. ...DNA fragmentation factor 45kDa, middle domain / DNA fragmentation factor 45 / DNA fragmentation factor 45kDa, C-terminal / DNA Fragmentation factor 45kDa, C terminal domain / DNA fragmentation factor 40, C-terminal / DNA fragmentation factor 40 / DNA fragmentation factor 40 kDa / CIDE-N domain / CIDE-N domain / CIDE-N domain profile. / Domains present in proteins implicated in post-mortem DNA fragmentation / Ubiquitin-like (UB roll) - #10 / His-Me finger superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
DNA fragmentation factor subunit alpha / DNA fragmentation factor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsOtomo, T. / Sakahira, H. / Uegaki, K. / Nagata, S. / Yamazaki, T.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the heterodimeric complex between CAD domains of CAD and ICAD.
Authors: Otomo, T. / Sakahira, H. / Uegaki, K. / Nagata, S. / Yamazaki, T.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of the CAD Domain of Caspase-Activated DNase and Interaction with the CAD Domain of its Inhibitor.
Authors: Uegaki, K. / Otomo, T. / Sakahira, H. / Shimizu, M. / Yumoto, N. / Kyogoku, Y. / Nagata, S. / Yamazaki, T.
#2: Journal: Nature / Year: 1998
Title: A Caspase-Activated DNase that Degrades DNA During Apoptosis, and its Inhibitor ICAD.
Authors: Enari, M. / Sakahira, H. / Yokoyama, H. / Okawa, K. / Iwamatsu, A. / Nagata, S.
#3: Journal: Nature / Year: 1998
Title: Cleavage of CAD Inhibitor in CAD Activation and DNA Degradation During Apoptosis.
Authors: Sakahira, H. / Enari, M. / Nagata, S.
History
DepositionMay 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: CASPASE-ACTIVATED DNASE
I: INHIBITOR OF CASPASE-ACTIVATED DNASE


Theoretical massNumber of molelcules
Total (without water)20,6902
Polymers20,6902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein CASPASE-ACTIVATED DNASE /


Mass: 9613.200 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN (CAD DOMAIN), RESIDUES 1-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / References: UniProt: O54788
#2: Protein INHIBITOR OF CASPASE-ACTIVATED DNASE


Mass: 11076.416 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN (CAD DOMAIN), RESIDUES 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / References: UniProt: O54786

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
1243D 13C-separated NOESY
1313D 15N-separated NOESY
1433D 15N-separated NOESY
1524D 13C-separated NOESY
1644D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM CAD U-15N,13C/0.6mM ICAD unlabeled; 20mM phophate buffer pH6.490% H2O/10% D2O
20.6mM CAD U-15N,13C/0.6mM ICAD unlabeled; 20mM phophate buffer pH6.4100% D2O
30.6mM ICAD U-15N,13C/0.6mM CAD unlabeled; 20mM phophate buffer pH6.490% H2O/10% D2O
40.6mM ICAD U-15N,13C/0.6mM CAD unlabeled; 20mM phophate buffer pH6.4100% D2O
Sample conditionsIonic strength: 0 / pH: 6.4 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.841Brungerstructure solution
X-PLOR3.841Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2646 restraints, 2503 are NOE-derived distance constraints, 93 dihedral angle restraints,50 distance restraints from hydrogen bonds.
NMR ensembleConformers submitted total number: 1

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