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- PDB-1z6t: Structure of the apoptotic protease-activating factor 1 bound to ADP -

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Basic information

Entry
Database: PDB / ID: 1z6t
TitleStructure of the apoptotic protease-activating factor 1 bound to ADP
ComponentsApoptotic protease activating factor 1
KeywordsAPOPTOSIS / Apaf-1 / caspase activation / ADP / nucleotide binding / CARD
Function / homology
Function and homology information


response to G1 DNA damage checkpoint signaling / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TP53 Regulates Transcription of Caspase Activators and Caspases ...response to G1 DNA damage checkpoint signaling / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / forebrain development / positive regulation of apoptotic signaling pathway / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / intrinsic apoptotic signaling pathway / response to nutrient / kidney development / neural tube closure / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / neuron apoptotic process / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / positive regulation of apoptotic process / nucleotide binding / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Helical domain of apoptotic protease-activating factors / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #370 / Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / Death Domain, Fas ...Helical domain of apoptotic protease-activating factors / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #370 / Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / G-protein beta WD-40 repeat / WD40 repeat, conserved site / P-loop containing nucleotide triphosphate hydrolases / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Apoptotic protease-activating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å
AuthorsRiedl, S.J. / Li, W. / Chao, Y. / Schwarzenbacher, R. / Shi, Y.
CitationJournal: Nature / Year: 2005
Title: Structure of the apoptotic protease-activating factor 1 bound to ADP
Authors: Riedl, S.J. / Li, W. / Chao, Y. / Schwarzenbacher, R. / Shi, Y.
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / 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.end_auth_comp_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: Apoptotic protease activating factor 1
B: Apoptotic protease activating factor 1
C: Apoptotic protease activating factor 1
D: Apoptotic protease activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,1298
Polymers271,4204
Non-polymers1,7094
Water14,466803
1
A: Apoptotic protease activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2822
Polymers67,8551
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptotic protease activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2822
Polymers67,8551
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Apoptotic protease activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2822
Polymers67,8551
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Apoptotic protease activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2822
Polymers67,8551
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.955, 92.883, 94.988
Angle α, β, γ (deg.)62.96, 89.99, 90.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA106 - 350106 - 350
21ILEILEPHEPHEBB106 - 350106 - 350
31ILEILEPHEPHECC106 - 350106 - 350
41ILEILEPHEPHEDD106 - 350106 - 350
52ASPASPGLNGLNAA360 - 586360 - 586
62ASPASPGLNGLNBB360 - 586360 - 586
72ASPASPGLNGLNCC360 - 586360 - 586
82ASPASPGLNGLNDD360 - 586360 - 586

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Components

#1: Protein
Apoptotic protease activating factor 1 / Apaf-1


Mass: 67855.008 Da / Num. of mol.: 4 / Fragment: Apaf-1, residues 1-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14727
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 803 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 276 K / pH: 7.1
Details: HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONCHESS A110.954
SYNCHROTRONCHESS A121.0088, 0.9500, 1.0053
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1X25SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21.00881
30.951
41.00531
ReflectionResolution: 2.2→50 Å / Num. obs: 103300 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 12.7
Reflection shellResolution: 2.21→2.27 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.267 / % possible all: 48.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.21→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS UNACCOUNTED DENSITY NEXT TO CYSTEINES A115, A450; B115,B450;C115,C450;D115,D450;
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5211 5.1 %RANDOM
Rwork0.189 ---
obs0.192 97722 89.2 %-
all-102933 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.13 Å20.77 Å2
2--0.4 Å2-0.45 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.21→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18752 0 108 803 19663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02219376
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217608
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.97726160
X-RAY DIFFRACTIONr_angle_other_deg0.872341224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19152340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38224.73888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.481153676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.50315100
X-RAY DIFFRACTIONr_chiral_restr0.0780.22904
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221084
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023716
X-RAY DIFFRACTIONr_nbd_refined0.2090.24397
X-RAY DIFFRACTIONr_nbd_other0.1810.217362
X-RAY DIFFRACTIONr_nbtor_refined0.1750.29294
X-RAY DIFFRACTIONr_nbtor_other0.0880.210713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2856
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.230.25
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.262
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.19315178
X-RAY DIFFRACTIONr_mcbond_other0.23934724
X-RAY DIFFRACTIONr_mcangle_it2.682518904
X-RAY DIFFRACTIONr_scbond_it4.68789001
X-RAY DIFFRACTIONr_scangle_it6.432117256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2792tight positional0.050.05
2B2792tight positional0.050.05
3C2792tight positional0.050.05
4D2792tight positional0.050.05
1A4583medium positional0.460.5
2B4583medium positional0.460.5
3C4583medium positional0.420.5
4D4583medium positional0.510.5
1A2792tight thermal0.130.5
2B2792tight thermal0.130.5
3C2792tight thermal0.130.5
4D2792tight thermal0.130.5
1A4583medium thermal0.722
2B4583medium thermal0.712
3C4583medium thermal0.732
4D4583medium thermal0.722
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 197 -
Rwork0.243 3661 -
obs--46.1 %
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)
10.78020.153-0.36970.633-0.00180.4692-0.0240.0069-0.09220.0383-0.0563-0.03670.0715-0.05750.0803-0.0753-0.0153-0.050.01630.0085-0.1035-6.41239.21784.205
21.44460.5696-0.5441.0327-0.08990.4451-0.0417-0.01060.0104-0.0531-0.0019-0.12540.02680.03820.0436-0.1076-0.0254-0.0856-0.0230.0332-0.16-6.00962.5140.844
31.3781-0.54240.45491.083-0.13090.3923-0.0540.0054-0.01950.0542-0.0003-0.132-0.02740.0470.0544-0.0943-0.0476-0.0129-0.01980.0346-0.157131.924106.73941.546
41.017-0.20510.40610.81920.01430.5922-0.0343-0.01230.1344-0.0395-0.0782-0.0303-0.0953-0.07370.1126-0.0923-0.0595-0.0376-0.00250.0129-0.129731.52980.3382.789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 941 - 94
2X-RAY DIFFRACTION1AA105 - 586105 - 586
3X-RAY DIFFRACTION2BB1 - 1031 - 103
4X-RAY DIFFRACTION2BB104 - 586104 - 586
5X-RAY DIFFRACTION3CC1 - 1031 - 103
6X-RAY DIFFRACTION3CC104 - 586104 - 586
7X-RAY DIFFRACTION4DD1 - 941 - 94
8X-RAY DIFFRACTION4DD105 - 586105 - 586

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