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- PDB-4m9r: Crystal structure of CED-3 -

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Basic information

Entry
Database: PDB / ID: 4m9r
TitleCrystal structure of CED-3
ComponentsCell death protein 3
KeywordsHYDROLASE / caspase / protease / CED-4
Function / homology
Function and homology information


negative regulation of cellular response to manganese ion / positive regulation of cellular response to gamma radiation / Apoptotic cleavage of cellular proteins / Apoptosis induced DNA fragmentation / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of TNFR1 signaling / Apoptotic cleavage of cell adhesion proteins / positive regulation of egg-laying behavior ...negative regulation of cellular response to manganese ion / positive regulation of cellular response to gamma radiation / Apoptotic cleavage of cellular proteins / Apoptosis induced DNA fragmentation / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of TNFR1 signaling / Apoptotic cleavage of cell adhesion proteins / positive regulation of egg-laying behavior / regulation of vulval development / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / positive regulation of synapse pruning / caspase complex / caspase-7 / regulation of cell fate specification / positive regulation of protein processing / programmed cell death / apoptotic process involved in development / negative regulation of execution phase of apoptosis / actin filament depolymerization / activation of cysteine-type endopeptidase activity / cysteine-type endopeptidase activity involved in execution phase of apoptosis / embryo development ending in birth or egg hatching / execution phase of apoptosis / regulation of locomotion / muscle cell cellular homeostasis / regulation of synapse organization / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / regulation of cell adhesion / protein catabolic process / regulation of protein stability / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / presynapse / perikaryon / nuclear membrane / endopeptidase activity / defense response to Gram-negative bacterium / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / perinuclear region of cytoplasm / mitochondrion / proteolysis / membrane / identical protein binding / cytoplasm
Similarity search - Function
Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell death protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.656 Å
AuthorsXu, Y. / Jeffrey, P.D. / Shi, Y.G.
CitationJournal: Genes Dev. / Year: 2013
Title: Mechanistic insights into CED-4-mediated activation of CED-3
Authors: Huang, W. / Jiang, T. / Choi, W. / Qi, S. / Pang, Y. / Hu, Q. / Xu, Y. / Gong, X. / Jeffrey, P.D. / Wang, J. / Shi, Y.G.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cell death protein 3
B: Cell death protein 3


Theoretical massNumber of molelcules
Total (without water)69,4752
Polymers69,4752
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-17 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.070, 121.070, 58.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11segid A and resid 208:315
21segid B and resid 208:315
12segid A and resid 320:337
22segid B and resid 320:337
13segid A and resid 338:357
23segid B and resid 338:357
14segid A and resid 370:418
24segid B and resid 370:418
15segid A and resid 437:468
25segid B and resid 437:468
16segid A and resid 481:500
26segid B and resid 481:500

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth seq-ID
111segid A and resid 208:315208 - 315
211segid B and resid 208:315208 - 315
112segid A and resid 320:337320 - 337
212segid B and resid 320:337320 - 337
113segid A and resid 338:357338 - 357
213segid B and resid 338:357338 - 357
114segid A and resid 370:418370 - 418
214segid B and resid 370:418370 - 418
115segid A and resid 437:468437 - 468
215segid B and resid 437:468437 - 468
116segid A and resid 481:500481 - 500
216segid B and resid 481:500481 - 500

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Cell death protein 3 / / CED-3 / Cell death protein 3 subunit 1 / Cell death protein 3 subunit 2


Mass: 34737.500 Da / Num. of mol.: 2 / Fragment: UNP residues 198-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ced-3 / Production host: Escherichia coli (E. coli)
References: UniProt: P42573, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.542 Å3/Da / Density % sol: 20.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 20%(w/v) PEG3350, 0.2M (NH4)2SO4 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2005 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→20.178 Å / Num. all: 12370 / Num. obs: 11999 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 65.44 Å2
Reflection shellResolution: 2.65→2.92 Å / % possible all: 89.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CP3

1cp3


Resolution: 2.656→20.178 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7752 / SU ML: 0.42 / σ(F): 1.35 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 576 4.8 %random
Rwork0.2062 ---
all0.2088 12338 --
obs0.2088 11997 97.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.247 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 215.83 Å2 / Biso mean: 82.168 Å2 / Biso min: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.8377 Å20 Å2-0 Å2
2--9.8377 Å20 Å2
3----19.6754 Å2
Refinement stepCycle: LAST / Resolution: 2.656→20.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 0 7 3821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053894
X-RAY DIFFRACTIONf_angle_d0.8345259
X-RAY DIFFRACTIONf_chiral_restr0.058587
X-RAY DIFFRACTIONf_plane_restr0.004679
X-RAY DIFFRACTIONf_dihedral_angle_d16.0171432
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A873X-RAY DIFFRACTIONTORSIONAL0.402
12B873X-RAY DIFFRACTIONTORSIONAL0.402
21A141X-RAY DIFFRACTIONTORSIONAL0.221
22B141X-RAY DIFFRACTIONTORSIONAL0.221
31A150X-RAY DIFFRACTIONTORSIONAL0.373
32B150X-RAY DIFFRACTIONTORSIONAL0.373
41A87X-RAY DIFFRACTIONTORSIONAL0.514
42B87X-RAY DIFFRACTIONTORSIONAL0.514
51A244X-RAY DIFFRACTIONTORSIONAL0.264
52B244X-RAY DIFFRACTIONTORSIONAL0.264
61A178X-RAY DIFFRACTIONTORSIONAL0.446
62B178X-RAY DIFFRACTIONTORSIONAL0.446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6564-2.92310.35821360.29952745288194
2.9231-3.34440.27991550.23872853300899
3.3444-4.20730.25491310.18022912304399
4.2073-20.17890.23871540.19352911306598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.80920.79630.56573.0861-0.51042.6446-0.0291-0.34430.22840.38950.0796-0.0983-0.15790.1506-0.04130.52020.0064-0.05250.5711-0.13420.43272.3678-23.017534.5774
22.50250.47521.37863.59751.2083.4766-0.0738-0.08120.32260.09840.0033-0.0332-0.3777-0.40740.08520.52870.0330.0420.5185-0.13450.4722-2.4143-24.892824.3551
33.05230.2948-0.99992.0339-0.653.3305-0.07240.1283-0.0119-0.58280.1664-0.15180.48920.053-0.05260.72560.00670.06230.4945-0.18830.53211.7198-39.32793.1908
42.43080.2105-0.36132.21510.60242.32670.0967-0.0719-0.0401-0.2095-0.0772-0.11930.4509-0.1354-0.03050.5868-0.0313-0.01140.4443-0.0440.4058-1.8906-38.003112.2196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 208:337)A208 - 337
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 338:500)A338 - 500
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 208:337)B208 - 337
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 338:500)B338 - 500

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