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- PDB-1ddb: STRUCTURE OF MOUSE BID, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ddb
TitleSTRUCTURE OF MOUSE BID, NMR, 20 STRUCTURES
ComponentsPROTEIN (BID)
KeywordsAPOPTOSIS / PROGRAMMED CELL DEATH / BCL-2 FAMILY / BH3 DOMAIN
Function / homology
Function and homology information


Activation, myristolyation of BID and translocation to mitochondria / positive regulation of autophagy in response to ER overload / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation of BAD and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mitochondrial outer membrane permeabilization / positive regulation of fibroblast apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion ...Activation, myristolyation of BID and translocation to mitochondria / positive regulation of autophagy in response to ER overload / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation of BAD and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mitochondrial outer membrane permeabilization / positive regulation of fibroblast apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion / regulation of epithelial cell proliferation / establishment of protein localization to membrane / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of T cell proliferation / hepatocyte apoptotic process / regulation of G1/S transition of mitotic cell cycle / apoptotic mitochondrial changes / positive regulation of release of cytochrome c from mitochondria / mitochondrial ATP synthesis coupled electron transport / signal transduction in response to DNA damage / supramolecular fiber organization / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / mitochondrial membrane / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / protein-containing complex assembly / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / mitochondrion / membrane / cytosol
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BH3-interacting domain death agonist
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry
AuthorsMcdonnell, J.M. / Fushman, D. / Milliman, C. / Korsmeyer, S.J. / Cowburn, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Solution structure of the proapoptotic molecule BID: a structural basis for apoptotic agonists and antagonists.
Authors: McDonnell, J.M. / Fushman, D. / Milliman, C.L. / Korsmeyer, S.J. / Cowburn, D.
History
DepositionFeb 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: 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
A: PROTEIN (BID)


Theoretical massNumber of molelcules
Total (without water)21,9751
Polymers21,9751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN (BID)


Mass: 21974.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BID / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P70444

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N)HSQC
121(1H-13C)HSQC
131HSQC-J
1412D AND 3D 15N-NOESY-HMQC AND TOCSY-HMQC
15113C-NOESY-HMQC
161(H)CCH-TOCSY
171HNCA
181HN(CO)CA
191CBCANH
1101CBCA(CO)NH
1111HNCO
1121HN(CA)CO
1131(1H)15N-NOE
1141H2O-SELECTIVE 15N-EDITED NOESY AND ROESY
1151HYDROGEN-DEUTERIUM EXCHANGE
NMR detailsText: COORDINATES WERE CALCULATED FROM SOLUTION NMR DATA USING THE PROGRAM DYANA.

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Sample preparation

Sample conditionsIonic strength: 150mM / pH: 6.0 / Pressure: 1 atm / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6006001
Bruker DMX500BrukerDMX5005002

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
XwinNMRstructure solution
XEASYstructure solution
DIANAstructure solution
DYANAstructure solution
THE ECEPP LIBRARY WAS USEDstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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