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- PDB-3crd: NMR STRUCTURE OF THE RAIDD CARD DOMAIN, 15 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 3crd
TitleNMR STRUCTURE OF THE RAIDD CARD DOMAIN, 15 STRUCTURES
ComponentsRAIDD
KeywordsCASPASE RECRUITMENT DOMAIN / APOPTOSIS / HOMOPHILIC INTERACTION
Function / homology
Function and homology information


death domain binding / endopeptidase complex / TP53 Regulates Transcription of Caspase Activators and Caspases / extrinsic apoptotic signaling pathway via death domain receptors / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / cellular response to mechanical stimulus / protein-macromolecule adaptor activity / protease binding ...death domain binding / endopeptidase complex / TP53 Regulates Transcription of Caspase Activators and Caspases / extrinsic apoptotic signaling pathway via death domain receptors / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / cellular response to mechanical stimulus / protein-macromolecule adaptor activity / protease binding / positive regulation of apoptotic process / DNA damage response / nucleolus / nucleus / cytosol / cytoplasm
Similarity search - Function
CRADD, Death domain / Death domain-containing protein CRADD / RAIDD, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Death domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain ...CRADD, Death domain / Death domain-containing protein CRADD / RAIDD, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Death domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death domain-containing protein CRADD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsChou, J.J. / Matsuo, H. / Duan, H. / Wagner, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment.
Authors: Chou, J.J. / Matsuo, H. / Duan, H. / Wagner, G.
History
DepositionJul 24, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAIDD


Theoretical massNumber of molelcules
Total (without water)11,4531
Polymers11,4531
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 / 20LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
RepresentativeModel #3

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Components

#1: Protein RAIDD


Mass: 11453.228 Da / Num. of mol.: 1 / Fragment: CARD DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: HHHHHH HISTIDINE TAG WAS ADDED AT THE C-TERMINUS FOR EASE OF PURIFICATION
Production host: Escherichia coli (E. coli) / References: UniProt: P78560

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY (1H
12113C
13115N)
14115N TOCSY-HSQC
1512D TOCSY
161HCCHTOCSY
171HNCA
181HN(CO)CA
191HN(CA)CB
1101HN(CO)CACB
1111HNCO
1121HN(CA)CO

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Sample preparation

DetailsContents: TRIS
Sample conditionspH: 8.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUS750VarianUNITYPLUS7507501
Varian UNITY500VarianUNITY5005002
Varian UNITYPLUS500VarianUNITYPLUS5005003

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 15

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