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- PDB-4m9y: Crystal structure of CED-4 bound CED-3 fragment -

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Basic information

Entry
Database: PDB / ID: 4m9y
TitleCrystal structure of CED-4 bound CED-3 fragment
Components
  • CED-3 fragment
  • Cell death protein 4
KeywordsAPOPTOSIS / apoptosome
Function / homology
Function and homology information


BH1 domain binding / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / caspase complex / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / caspase binding / positive regulation of protein processing / embryonic morphogenesis / apoptotic process involved in development ...BH1 domain binding / positive regulation of apoptotic process involved in development / regulation of development, heterochronic / caspase complex / positive regulation of synapse pruning / peptidase activator activity involved in apoptotic process / caspase binding / positive regulation of protein processing / embryonic morphogenesis / apoptotic process involved in development / activation of cysteine-type endopeptidase activity / negative regulation of execution phase of apoptosis / actin filament depolymerization / embryo development ending in birth or egg hatching / regulation of cell size / muscle cell cellular homeostasis / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / endopeptidase activator activity / regulation of cell adhesion / ADP binding / regulation of protein stability / : / defense response to Gram-negative bacterium / positive regulation of apoptotic process / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / mitochondrion / ATP binding / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
Apoptosis regulator, Ced-4 / : / CED4, winged-helix domain / Caspase recruitment domain / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily ...Apoptosis regulator, Ced-4 / : / CED4, winged-helix domain / Caspase recruitment domain / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
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: 4.2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)130,6088
Polymers129,5454
Non-polymers1,0634
Water00
1
A: Cell death protein 4
C: CED-3 fragment
B: Cell death protein 4
D: CED-3 fragment
hetero molecules

A: Cell death protein 4
C: CED-3 fragment
B: Cell death protein 4
D: CED-3 fragment
hetero molecules

A: Cell death protein 4
C: CED-3 fragment
B: Cell death protein 4
D: CED-3 fragment
hetero molecules

A: Cell death protein 4
C: CED-3 fragment
B: Cell death protein 4
D: CED-3 fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,43132
Polymers518,17916
Non-polymers4,25216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area47300 Å2
ΔGint-206 kcal/mol
Surface area174700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.129, 181.129, 202.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Cell death protein 4


Mass: 63797.398 Da / Num. of mol.: 2
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: 975.024 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#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
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: 3.2 Å3/Da / Density % sol: 61.53 %
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: 4.2→50 Å / Num. obs: 18110 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 4.2→4.35 Å / % possible all: 100

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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: 4.2→42.927 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 40.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 862 4.76 %RANDOM
Rwork0.247 ---
all0.2495 23416 --
obs0.2495 18110 77.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→42.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8285 0 64 0 8349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088504
X-RAY DIFFRACTIONf_angle_d1.60311500
X-RAY DIFFRACTIONf_dihedral_angle_d19.0473213
X-RAY DIFFRACTIONf_chiral_restr0.0631315
X-RAY DIFFRACTIONf_plane_restr0.0081464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.2003-4.46320.32611020.2585202455
4.4632-4.80740.26131070.2348241664
4.8074-5.29040.3051380.2386263972
5.2904-6.05410.30141690.2597300181
6.0541-7.62050.40131540.3087348593
7.6205-42.92910.27611920.2311368399

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