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- PDB-1ty4: Crystal structure of a CED-9/EGL-1 complex -

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Basic information

Entry
Database: PDB / ID: 1ty4
TitleCrystal structure of a CED-9/EGL-1 complex
Components
  • Apoptosis regulator ced-9
  • EGg Laying defective EGL-1, programmed cell death activator
KeywordsAPOPTOSIS / CED-9 / EGL-1 / Bcl-2 family proteins / recognition
Function / homology
Function and homology information


BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / regulation of development, heterochronic / positive regulation of apoptotic process involved in development / positive regulation of synapse pruning / positive regulation of mitochondrial fusion / apoptotic process involved in development / actin filament depolymerization / negative regulation of execution phase of apoptosis / positive regulation of programmed cell death ...BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / regulation of development, heterochronic / positive regulation of apoptotic process involved in development / positive regulation of synapse pruning / positive regulation of mitochondrial fusion / apoptotic process involved in development / actin filament depolymerization / negative regulation of execution phase of apoptosis / positive regulation of programmed cell death / negative regulation of programmed cell death / apoptotic mitochondrial changes / regulation of synapse organization / organelle membrane / negative regulation of protein-containing complex assembly / mitophagy / extrinsic apoptotic signaling pathway in absence of ligand / endomembrane system / GTPase activator activity / protein sequestering activity / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / protein processing / 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 / intracellular membrane-bounded organelle / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / membrane / cytosol / cytoplasm
Similarity search - Function
Programmed cell death activator EGL-1 / Programmed cell death activator EGL-1 / 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 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. ...Programmed cell death activator EGL-1 / Programmed cell death activator EGL-1 / 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 / Blc2-like / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death activator egl-1 / Apoptosis regulator ced-9
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYan, N. / Gu, L. / Kokel, D. / Xue, D. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2004
Title: Structural, Biochemical, and Functional Analyses of CED-9 Recognition by the Proapoptotic Proteins EGL-1 and CED-4
Authors: Yan, N. / Gu, L. / Kokel, D. / Chai, J. / Li, W. / Han, A. / Chen, L. / Xue, D. / Shi, Y.
History
DepositionJul 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator ced-9
B: Apoptosis regulator ced-9
C: EGg Laying defective EGL-1, programmed cell death activator
D: EGg Laying defective EGL-1, programmed cell death activator


Theoretical massNumber of molelcules
Total (without water)53,5324
Polymers53,5324
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Apoptosis regulator ced-9
C: EGg Laying defective EGL-1, programmed cell death activator


Theoretical massNumber of molelcules
Total (without water)26,7662
Polymers26,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-28 kcal/mol
Surface area9580 Å2
MethodPISA, PQS
3
B: Apoptosis regulator ced-9
D: EGg Laying defective EGL-1, programmed cell death activator


Theoretical massNumber of molelcules
Total (without water)26,7662
Polymers26,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-28 kcal/mol
Surface area9310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.713, 93.713, 57.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 20315.746 Da / Num. of mol.: 2 / Fragment: BH1,BH2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ced-9,T07C4.8 / Plasmid: pGEX-2T,pBB75 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41958
#2: Protein EGg Laying defective EGL-1, programmed cell death activator


Mass: 6450.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pGEX-2T,pBB75 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O61667
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium cacodylate, isopropanol, magnesium acatate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. all: 25502 / Num. obs: 25359 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rsym value: 0.084
Reflection shellResolution: 2.2→2.28 Å / Rsym value: 0.495 / % possible all: 99.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 2458 RANDOM
Rwork0.212 --
all0.22 25502 -
obs0.22 24864 -
Solvent computationBsol: 45.3891 Å2 / ksol: 0.348538 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.146 Å20 Å20 Å2
2---3.146 Å20 Å2
3---6.292 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 0 67 3136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_mcbond_it2.2991.5
X-RAY DIFFRACTIONc_scbond_it3.422
X-RAY DIFFRACTIONc_mcangle_it4.0022
X-RAY DIFFRACTIONc_scangle_it5.5272.5
LS refinement shellResolution: 2.2→2.28 Å / Num. reflection obs: 2514
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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