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- PDB-2a5y: Structure of a CED-4/CED-9 complex -

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Basic information

Entry
Database: PDB / ID: 2a5y
TitleStructure of a CED-4/CED-9 complex
Components
  • Apoptosis regulator ced-9
  • ced-4
KeywordsAPOPTOSIS / CED-4 / CED-9 / CED-3 activation
Function / homology
Function and homology information


BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / BH1 domain binding / regulation of development, heterochronic / caspase complex / positive regulation of apoptotic process involved in development / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / caspase binding / positive regulation of mitochondrial fusion ...BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / BH1 domain binding / regulation of development, heterochronic / caspase complex / positive regulation of apoptotic process involved in development / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / caspase binding / positive regulation of mitochondrial fusion / positive regulation of protein processing / embryonic morphogenesis / cysteine-type endopeptidase activator activity / apoptotic process involved in development / actin filament depolymerization / negative regulation of execution phase of apoptosis / embryo development ending in birth or egg hatching / negative regulation of programmed cell death / cysteine-type endopeptidase activator activity involved in apoptotic process / muscle cell cellular homeostasis / regulation of cell size / regulation of synapse organization / organelle membrane / BH3 domain binding / endopeptidase activator activity / negative regulation of protein-containing complex assembly / regulation of cell adhesion / mitophagy / extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / GTPase activator activity / protein sequestering activity / release of cytochrome c from mitochondria / regulation of protein stability / protein processing / ADP binding / intrinsic apoptotic signaling pathway in response to DNA damage / presynapse / channel activity / defense response to Gram-negative bacterium / perikaryon / mitochondrial outer membrane / positive regulation of apoptotic process / neuronal cell body / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / mitochondrion / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Ced-4 linker helical domain-like / : / CED4, winged-helix domain / Caspase recruitment domain / Death Domain, Fas / Death Domain, Fas / NB-ARC / NB-ARC domain / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 ...Ced-4 linker helical domain-like / : / CED4, winged-helix domain / Caspase recruitment domain / Death Domain, Fas / Death Domain, Fas / NB-ARC / NB-ARC domain / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / CARD domain / CARD caspase recruitment domain profile. / Blc2-like / Caspase recruitment domain / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Death-like domain superfamily / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cell death protein 4 / Apoptosis regulator ced-9
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsYan, N. / Liu, Q. / Hao, Q. / Gu, L. / Shi, Y.
CitationJournal: Nature / Year: 2005
Title: Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans.
Authors: Yan, N. / Chai, J. / Lee, E.S. / Gu, L. / Liu, Q. / He, J. / Wu, J.W. / Kokel, D. / Li, H. / Hao, Q. / Xue, D. / Shi, Y.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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
A: Apoptosis regulator ced-9
B: ced-4
C: ced-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,6907
Polymers149,6273
Non-polymers1,0634
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-53 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.898, 128.898, 209.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Apoptosis regulator ced-9 / Cell death protein 9


Mass: 23720.908 Da / Num. of mol.: 1 / Fragment: residues 48-251 / Mutation: C107S, C135S, C164S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41958
#2: Protein ced-4


Mass: 62953.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P30429
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, HEPES, Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9645
SYNCHROTRONNSLS X2520.9791, 0.9794, 0.9600
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 1, 2004
ADSC QUANTUM 42CCDSep 30, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.96451
20.97911
30.97941
40.961
ReflectionResolution: 2.6→50 Å / Num. all: 55095 / Num. obs: 54599 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.6→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 2433 random
Rwork0.249 --
all0.25 55027 -
obs0.249 52166 -
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 64 260 8730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.49

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