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- PDB-3lqr: Structure of CED-4:CED-3 complex -

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Basic information

Entry
Database: PDB / ID: 3lqr
TitleStructure of CED-4:CED-3 complex
ComponentsCell death protein 4
KeywordsAPOPTOSIS / CED-4 / CED-3 / 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 / 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: 3.896 Å
AuthorsQi, S. / Pang, Y. / Shi, Y. / Yan, N.
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 / 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 / _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 area29980 Å2
ΔGint-52 kcal/mol
Surface area176900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.33, 181.33, 202.88
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
111METMETASNASNchain A and (resseq 1:96 )AA1 - 961 - 96
211METMETASNASNchain B and (resseq 1:96 )BB1 - 961 - 96
112GLYGLYSERSERchain A and (resseq 122:292 )AA122 - 292122 - 292
212GLYGLYSERSERchain B and (resseq 122:292 )BB122 - 292122 - 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 details: CED-3 were expressed or co-expressed in E. coli BL21(DE3).
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
Compound detailsTHIS ENTRY IS FOR A COMPLEX OF CED-4:CED-3. HOWEVER, CED-3 CAN NOT SEE DUE TO POOR DENSITY, AND IT ...THIS ENTRY IS FOR A COMPLEX OF CED-4:CED-3. HOWEVER, CED-3 CAN NOT SEE DUE TO POOR DENSITY, AND IT IS MISSING IN THIS ENTRY.
Sequence detailsTHE SEQUENCE MATCHES TO ISOFORM A OF UNIPROT ENTRY CED4_CAEEL (IDENTIFIER: P30429-2). THE SEQUENCE ...THE SEQUENCE MATCHES TO ISOFORM A OF UNIPROT ENTRY CED4_CAEEL (IDENTIFIER: P30429-2). THE SEQUENCE OF CED-3 IS TQYIFHEEDMNFVDAPTISRVFDEKTMYRNFSSPRGMCLIINNEHFEQMPTRNSTKADK DNLTNLFRCMGYTVICKDNLTGRGMLLTIRDFAKHESHGDSAILVILSHGEENVIIGVD DIPISTHEIYDLLNAANAPRLANKPKIVFVQASRGERRDNGFPVRKKPSQADILIAYAT TAQYVSWRNSARGSWFIQAVCEVFSTHAKDMDVVELLTEVNKKVACGFQTSQGSNILKQ MPEMTSRLLKKFYFWPEARN.

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 0.6-0.8M potassium sodium tartrate tetrahydrate, 0.1M guanidine-HCl, 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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.896→39.776 Å / Num. obs: 15624 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 143.28 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 18
Reflection shellResolution: 3.896→4.04 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.75 / Num. unique all: 1539 / Rsym value: 0.883 / % possible all: 99.5

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Processing

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

2a5y


Resolution: 3.896→39.776 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.604 / SU ML: 0.67 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 42.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 689 4.53 %Thin Shell
Rwork0.2552 14523 --
obs0.2569 15212 96.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 162.364 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 440.25 Å2 / Biso mean: 196.163 Å2 / Biso min: 82.74 Å2
Baniso -1Baniso -2Baniso -3
1-20.164 Å20 Å2-0 Å2
2--20.164 Å20 Å2
3----40.328 Å2
Refinement stepCycle: LAST / Resolution: 3.896→39.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 64 0 8124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098608
X-RAY DIFFRACTIONf_angle_d1.58111532
X-RAY DIFFRACTIONf_dihedral_angle_d20.873114
X-RAY DIFFRACTIONf_chiral_restr0.0821286
X-RAY DIFFRACTIONf_plane_restr0.0051426
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A798X-RAY DIFFRACTIONPOSITIONAL0.035
12B798X-RAY DIFFRACTIONPOSITIONAL0.035
21A1359X-RAY DIFFRACTIONPOSITIONAL0.035
22B1359X-RAY DIFFRACTIONPOSITIONAL0.035
31A1659X-RAY DIFFRACTIONPOSITIONAL0.033
32B1659X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8963-4.19690.34092892X-RAY DIFFRACTION94
4.1969-4.61860.37083090.29012660X-RAY DIFFRACTION96
4.6186-5.28560.24423021X-RAY DIFFRACTION97
5.2856-6.65430.37562350.25662881X-RAY DIFFRACTION99
6.6543-39.77840.20651450.22523069X-RAY DIFFRACTION97
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)
10.45580.74420.58370.1434-0.5242-0.5154-0.16910.50630.8815-0.41210.41820.3983-1.06510.3391-0.00012.2264-0.0544-0.15722.47740.18291.695616.8752-21.86571.551
20.4605-0.0378-0.27790.1964-0.5575-0.5427-0.3104-0.1713-0.72540.2336-0.1590.12570.6575-0.0152-0.00152.69020.22150.10412.77240.33361.93-3.5097-26.045888.1356
30.7258-0.1349-0.21310.28410.78281.49160.0259-0.7538-0.1810.2736-0.1557-0.08110.60030.4468-0.00011.15920.0625-0.13420.82960.17121.076920.1897-35.345245.0991
41.09930.14360.5710.85180.87971.9658-0.2885-0.23630.20790.0135-0.058-0.09310.2197-0.06310.00030.9714-0.25530.11190.98720.13561.1246-10.5941-39.160745.0626
50.9477-0.1174-1.86150.47480.33411.0337-0.0280.18870.08570.59880.08510.31540.3707-0.0090.00041.69180.30470.0050.95820.08431.131320.9523-56.267621.4882
61.87750.5582-1.18110.57011.38151.17140.2983-0.02530.13780.3067-0.4222-0.10240.3386-0.1318-01.5614-0.318-0.00770.90070.09251.1063-25.2012-54.515921.7124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:96A1 - 96
2X-RAY DIFFRACTION2chain B and resid 1:96B1 - 96
3X-RAY DIFFRACTION3chain A and resid 122:292A122 - 292
4X-RAY DIFFRACTION4chain B and resid 122:292B122 - 292
5X-RAY DIFFRACTION5chain A and resid 293:543A293 - 543
6X-RAY DIFFRACTION6chain B and resid 293:543B293 - 543

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