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- PDB-4m9z: Crystal structure of CED-4 bound CED-3 fragment -

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Basic information

Entry
Database: PDB / ID: 4m9z
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 / 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 / apoptotic process involved in development ...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 / apoptotic process involved in development / cysteine-type endopeptidase activator activity / 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 / regulation of protein stability / ADP binding / 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 / membrane / nucleus / 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 / Helicase, Ruva Protein; domain 3 / Death-like domain superfamily / 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: 3.405 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 1.3Nov 13, 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)261,21616
Polymers259,0908
Non-polymers2,1268
Water00
1
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

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

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

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)1,044,86364
Polymers1,036,35932
Non-polymers8,50432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area101000 Å2
ΔGint-467 kcal/mol
Surface area337420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.167, 178.167, 200.738
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: 975.024 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: 3.07 Å3/Da / Density % sol: 59.99 %
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: 3.405→50 Å / Num. obs: 48180 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.405→3.7 Å / % possible all: 99.4

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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: 3.405→43.212 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 38.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3271 2405 4.99 %RANDOM
Rwork0.2695 ---
all0.2724 ---
obs0.2724 48180 56.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.405→43.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16559 0 128 0 16687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616996
X-RAY DIFFRACTIONf_angle_d1.53322984
X-RAY DIFFRACTIONf_dihedral_angle_d19.4676421
X-RAY DIFFRACTIONf_chiral_restr0.0612629
X-RAY DIFFRACTIONf_plane_restr0.0082926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4046-3.47410.5128350.346868615
3.4741-3.54960.3934360.346481817
3.5496-3.63210.446360.34198821
3.6321-3.72290.4346630.3144120025
3.7229-3.82350.395690.3124156333
3.8235-3.93590.33181060.3138191741
3.9359-4.06290.36221170.2978234549
4.0629-4.2080.3341200.2857270557
4.208-4.37630.30921430.279283560
4.3763-4.57520.33491640.253307265
4.5752-4.81620.30851850.2349326469
4.8162-5.11750.32691930.2394349274
5.1175-5.51190.31431980.2602368378
5.5119-6.06520.32782190.2771393584
6.0652-6.93970.34842170.3105421189
6.9397-8.73150.33542790.286451096
8.7315-43.21530.28722250.238455196

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