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- PDB-4m9s: crystal structure of CED-4 bound CED-3 fragment -

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Basic information

Entry
Database: PDB / ID: 4m9s
Titlecrystal structure of CED-4 bound CED-3 fragment
Components
  • CED-3 fragment
  • Cell death protein 4
KeywordsAPOPTOSIS / apoptosome / CED-3
Function / homology
Function and homology information


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 protein processing / embryonic morphogenesis / cysteine-type endopeptidase activator activity ...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 protein processing / embryonic morphogenesis / cysteine-type endopeptidase activator activity / apoptotic process involved in development / actin filament depolymerization / embryo development ending in birth or egg hatching / negative regulation of execution phase of apoptosis / cysteine-type endopeptidase activator activity involved in apoptotic process / muscle cell cellular homeostasis / regulation of cell size / BH3 domain binding / endopeptidase activator activity / regulation of cell adhesion / ADP binding / regulation of protein stability / defense response to Gram-negative bacterium / positive regulation of apoptotic process / 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
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 / CARD domain / CARD caspase recruitment domain profile. ...Ced-4 linker helical domain-like / : / CED4, winged-helix domain / Caspase recruitment domain / Death Domain, Fas / Death Domain, Fas / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.207 Å
AuthorsHuang, W.J. / Jinag, T.Y. / Choi, W.Y. / Wang, J.W. / 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.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell death protein 4
E: CED-3 fragment
B: Cell death protein 4
F: CED-3 fragment
C: Cell death protein 4
G: CED-3 fragment
D: Cell death protein 4
H: CED-3 fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,47516
Polymers259,3498
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-96 kcal/mol
Surface area94100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.814, 178.814, 201.125
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Cell death protein 4


Mass: 63797.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ced-4, C35D10.9 / Production host: Escherichia coli (E. coli) / References: UniProt: P30429
#2: Protein/peptide
CED-3 fragment


Mass: 1039.957 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationY
Sequence detailsSEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM A OF UNIPROT P30429 (CED4_CAEEL, IDENTIFIER: P30429-2).

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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: 3.1 Å3/Da / Density % sol: 60.32 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS and I_PLUS/MINUS COLUMNS
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6-0.8M sodium acetate, 0.1M HEPES (pH 7.5), 0.1M sodium fluoride , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97894 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 56679 / % possible obs: 74.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.2→3.31 Å / % possible all: 27.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LQQ

3lqq


Resolution: 3.207→40.849 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 38.79 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS and I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.3335 2849 5.03 %
Rwork0.2828 --
all0.2854 --
obs0.2854 56679 55.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.207→40.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16559 0 128 0 16687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01816996
X-RAY DIFFRACTIONf_angle_d2.34122980
X-RAY DIFFRACTIONf_dihedral_angle_d19.6436425
X-RAY DIFFRACTIONf_chiral_restr0.1032625
X-RAY DIFFRACTIONf_plane_restr0.0132926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2069-3.26210.5845250.426246010
3.2621-3.32140.4866270.383754111
3.3214-3.38530.4362410.447261613
3.3853-3.45430.5164410.401578016
3.4543-3.52940.4778470.399787918
3.5294-3.61150.4857480.510697220
3.6115-3.70170.5133820.3767161833
3.7017-3.80170.4843710.3877144530
3.8017-3.91350.4258950.3192197641
3.9135-4.03970.43071380.3525258653
4.0397-4.1840.38321830.3182317466
4.184-4.35130.35031780.2993348171
4.3513-4.54910.31231830.2812378778
4.5491-4.78860.32992190.2525405384
4.7886-5.08810.30532240.2682425988
5.0881-5.48010.34352250.2704444591
5.4801-6.030.33872800.2934452694
6.03-6.8990.32992480.324472197
6.899-8.67830.31332530.2678479999
8.6783-40.85250.25132410.2131471297

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