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- PDB-3lqq: Structure of the CED-4 Apoptosome -

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Basic information

Entry
Database: PDB / ID: 3lqq
TitleStructure of the CED-4 Apoptosome
ComponentsCell death protein 4
KeywordsAPOPTOSIS / CED4 / apoptosome / Alternative splicing / ATP-binding / Mitochondrion / Nucleotide-binding
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 / negative regulation of execution phase of apoptosis / embryo development ending in birth or egg hatching / 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 / 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: 3.534 Å
AuthorsQi, S. / Pang, Y. / Shi, Y. / Yan, N. / Liu, Q.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4.
Authors: Qi, S. / Pang, Y. / Hu, Q. / Liu, Q. / Li, H. / Zhou, Y. / He, T. / Liang, Q. / Liu, Y. / Yuan, X. / Luo, G. / Li, H. / Wang, J. / Yan, N. / Shi, Y.
History
DepositionFeb 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell death protein 4
B: Cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9706
Polymers125,9072
Non-polymers1,0634
Water00
1
A: Cell death protein 4
B: Cell death protein 4
hetero molecules

A: Cell death protein 4
B: Cell death protein 4
hetero molecules

A: Cell death protein 4
B: Cell death protein 4
hetero molecules

A: Cell death protein 4
B: Cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,87824
Polymers503,6268
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 area31160 Å2
ΔGint-44 kcal/mol
Surface area176260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.64, 181.64, 203.19
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPHEPHEchain A and (resseq 1:93 )AA1 - 931 - 93
211METMETPHEPHEchain B and (resseq 1:93 )BB1 - 931 - 93
112ARGARGSERSERchain A and (resseq 117:292 )AA117 - 292117 - 292
212ARGARGSERSERchain B and (resseq 117:292 )BB117 - 292117 - 292
113LEULEUVALVALchain A and (resseq 293:416 or resseq 424:487 or resseq 521:543 )AA293 - 416293 - 416
123GLUGLUILEILEchain A and (resseq 293:416 or resseq 424:487 or resseq 521:543 )AA424 - 487424 - 487
133GLUGLULEULEUchain A and (resseq 293:416 or resseq 424:487 or resseq 521:543 )AA521 - 543521 - 543
213LEULEUVALVALchain B and (resseq 293:416 or resseq 426:487 or resseq 521:543 )BB293 - 416293 - 416
223LEULEUILEILEchain B and (resseq 293:416 or resseq 426:487 or resseq 521:543 )BB426 - 487426 - 487
233GLUGLULEULEUchain B and (resseq 293:416 or resseq 426:487 or resseq 521:543 )BB521 - 543521 - 543

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cell death protein 4 / CED-4 Apoptosome


Mass: 62953.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ced-4 / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P30429
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
Sequence detailsTHE SEQUENCE MATCHES TO ISOFORM A OF UNIPROT ENTRY 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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 0.7M sodium potassium tartrate, 200mM Cymal-1 (Anatrace), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97623 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 3.534→28.664 Å / Num. obs: 20874 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 112.77 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 14.6
Reflection shellResolution: 3.53→3.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.78 / Num. unique all: 1951 / % possible all: 94.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2a5y

2a5y


Resolution: 3.534→28.664 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.63 / SU ML: 0.58 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 40.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3112 1031 4.95 %Thin Shell
Rwork0.2748 19788 --
obs0.2768 20819 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.515 Å2 / ksol: 0.256 e/Å3
Displacement parametersBiso max: 395.93 Å2 / Biso mean: 151.5 Å2 / Biso min: 66.2 Å2
Baniso -1Baniso -2Baniso -3
1-21.32 Å20 Å2-0 Å2
2--21.32 Å20 Å2
3----42.639 Å2
Refinement stepCycle: LAST / Resolution: 3.534→28.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 64 0 8124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018608
X-RAY DIFFRACTIONf_angle_d1.43711532
X-RAY DIFFRACTIONf_dihedral_angle_d24.1775110
X-RAY DIFFRACTIONf_chiral_restr0.0841286
X-RAY DIFFRACTIONf_plane_restr0.0061426
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A777X-RAY DIFFRACTIONPOSITIONAL0.034
12B777X-RAY DIFFRACTIONPOSITIONAL0.034
21A1403X-RAY DIFFRACTIONPOSITIONAL0.04
22B1403X-RAY DIFFRACTIONPOSITIONAL0.04
31A1659X-RAY DIFFRACTIONPOSITIONAL0.035
32B1659X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5341-3.7200.38492800X-RAY DIFFRACTION94
3.72-3.95250.4813700.34652580X-RAY DIFFRACTION100
3.9525-4.256800.26622939X-RAY DIFFRACTION99
4.2568-4.68350.2852890.2262709X-RAY DIFFRACTION100
4.6835-5.357400.21262986X-RAY DIFFRACTION100
5.3574-6.73530.3372310.25362793X-RAY DIFFRACTION100
6.7353-28.66490.2331410.26192981X-RAY DIFFRACTION98

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