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- PDB-1ohu: Structure of Caenorhabditis elegans CED-9 -

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Basic information

Entry
Database: PDB / ID: 1ohu
TitleStructure of Caenorhabditis elegans CED-9
ComponentsAPOPTOSIS REGULATOR CED-9
KeywordsAPOPTOSIS / CED-9 / BCL-2 FAMILY
Function / homology
Function and homology information


BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / positive regulation of brood size / positive regulation of egg-laying behavior / positive regulation of fertilization / positive regulation of synapse pruning / positive regulation of mitochondrial fusion / positive regulation of embryonic development / apoptotic process involved in development / negative regulation of execution phase of apoptosis ...BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / positive regulation of brood size / positive regulation of egg-laying behavior / positive regulation of fertilization / positive regulation of synapse pruning / positive regulation of mitochondrial fusion / positive regulation of embryonic development / apoptotic process involved in development / negative regulation of execution phase of apoptosis / actin filament depolymerization / negative regulation of programmed cell death / regulation of synapse organization / organelle membrane / mitophagy / endomembrane system / negative regulation of protein-containing complex assembly / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / protein sequestering activity / GTPase activator activity / protein processing / intrinsic apoptotic signaling pathway in response to DNA damage / presynapse / perikaryon / defense response to Gram-negative bacterium / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / neuronal cell body / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / membrane / cytoplasm
Similarity search - Function
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family ...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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator ced-9
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.03 Å
AuthorsJeong, J.-S. / Ha, N.-C. / Oh, B.-H.
CitationJournal: Cell Death Differ. / Year: 2003
Title: Unique Structural Features of a Bcl-2 Family Protein Ced-9 and Biophysical Characterization of Ced-9/Egl-1 Interactions
Authors: Woo, J.-S. / Jung, J.-S. / Ha, N.-C. / Shin, J. / Kim, K.-H. / Lee, W. / Oh, B.-H.
History
DepositionMay 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOSIS REGULATOR CED-9
B: APOPTOSIS REGULATOR CED-9


Theoretical massNumber of molelcules
Total (without water)41,6262
Polymers41,6262
Non-polymers00
Water1,09961
1
A: APOPTOSIS REGULATOR CED-9


Theoretical massNumber of molelcules
Total (without water)20,8131
Polymers20,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: APOPTOSIS REGULATOR CED-9


Theoretical massNumber of molelcules
Total (without water)20,8131
Polymers20,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.790, 92.050, 47.640
Angle α, β, γ (deg.)90.00, 99.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APOPTOSIS REGULATOR CED-9 / CED-9 / CELL DEATH PROTEIN 9


Mass: 20813.158 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41958
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATIONS: CHAINS A, B CYS107SER, CYS135SER, CYS164SER

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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: 2.7 Å3/Da / Density % sol: 53.4 %
Crystal growpH: 7.5 / Details: 10% PEG 8K ,0.1M HEPES PH7.5, pH 7.50
Crystal grow
*PLUS
Temperature: 285 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %PEG80001reservoir
20.1 MHEPES1reservoirpH7.5
310 mg/mlprotein1drop
420 mMsodium phosphate1drop
550 mM1dropNaCl
62 mMbeta-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97921
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 21636 / % possible obs: 84.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.7
Reflection
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 54.2 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 2.3

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.03→30 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1055 5 %RANDOM
Rwork0.212 ---
obs0.212 21636 84.1 %-
Refinement stepCycle: LAST / Resolution: 2.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 0 61 2718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.089
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.0895

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