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- PDB-1d4b: CIDE-N DOMAIN OF HUMAN CIDE-B -

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Basic information

Entry
Database: PDB / ID: 1d4b
TitleCIDE-N DOMAIN OF HUMAN CIDE-B
ComponentsHUMAN CELL DEATH-INDUCING EFFECTOR B
KeywordsAPOPTOSIS / ALPHA/BETA ROLL
Function / homology
Function and homology information


: / activation of cysteine-type endopeptidase activity / bile acid signaling pathway / execution phase of apoptosis / positive regulation of release of cytochrome c from mitochondria / response to nutrient levels / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm ...: / activation of cysteine-type endopeptidase activity / bile acid signaling pathway / execution phase of apoptosis / positive regulation of release of cytochrome c from mitochondria / response to nutrient levels / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / identical protein binding / cytosol
Similarity search - Function
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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Cell death activator CIDE-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING TORSION ANGLE DYNAMICS RELAXATION DATA
AuthorsLugovskoy, A. / Zhou, P. / Chou, J. / McCarty, J. / Li, P. / Wagner, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis.
Authors: Lugovskoy, A.A. / Zhou, P. / Chou, J.J. / McCarty, J.S. / Li, P. / Wagner, G.
History
DepositionOct 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 1999Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN CELL DEATH-INDUCING EFFECTOR B


Theoretical massNumber of molelcules
Total (without water)13,7491
Polymers13,7491
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)15 / 30STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein HUMAN CELL DEATH-INDUCING EFFECTOR B / CIDE B


Mass: 13748.539 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHD4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: A MINIMAL SET OF NMR EXPERIMENTS REQUIRED FOR HIGH-RESOLUTION STRUCTURE DETERMINATION
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENTIONAL NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 0.5MM CIDE-N OF CIDE-B
Sample conditionsIonic strength: 0.15 / pH: 6.6 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Varian UNITYVarianUNITY5003
Varian INOVAVarianINOVA7504

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.18BRUNGERrefinement
DYANA1.5GUNTERTstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING TORSION ANGLE DYNAMICS RELAXATION DATA
Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 30 / Conformers submitted total number: 15

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