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- PDB-8xqk: The Crystal Structure of Apaf from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xqk
TitleThe Crystal Structure of Apaf from Biortus.
ComponentsApoptotic protease-activating factor 1
KeywordsAPOPTOSIS / Possesses tyrosine phosphatase activity. / HYDROLASE
Function / homology
Function and homology information


response to G1 DNA damage checkpoint signaling / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / 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 / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / 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 / 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 / positive regulation of apoptotic signaling pathway / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / regulation of apoptotic process / secretory granule lumen / neuron apoptotic process / 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
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 / NB-ARC / NB-ARC domain / CARD domain ...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 / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Apoptotic protease-activating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of Apaf from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.
History
DepositionJan 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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)45,1029
Polymers44,6274
Non-polymers4755
Water2,792155
1
A: Apoptotic protease-activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1571
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5130 Å2
MethodPISA
2
B: Apoptotic protease-activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3473
Polymers11,1571
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-6 kcal/mol
Surface area5590 Å2
MethodPISA
3
C: Apoptotic protease-activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1571
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5510 Å2
MethodPISA
4
D: Apoptotic protease-activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2522
Polymers11,1571
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.641, 75.336, 161.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111ILEILE0 - 911 - 92
211ILEILE0 - 911 - 92
322ILEILE0 - 911 - 92
422ILEILE0 - 911 - 92
533PROPRO0 - 921 - 93
633PROPRO0 - 921 - 93
744PROPRO0 - 921 - 93
844PROPRO0 - 921 - 93
955ILEILE0 - 911 - 92
1055ILEILE0 - 911 - 92
1166ILEILE0 - 911 - 92
1266ILEILE0 - 911 - 92

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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


Mass: 11156.761 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 / Production host: prokaryote coculture (bacteria) / References: UniProt: O14727
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M Na/KPO4 pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 1.85→48.75 Å / Num. obs: 18178 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 29.9
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.843 / Num. unique obs: 1113

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→37.696 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.864 / SU B: 23.186 / SU ML: 0.415 / Cross valid method: FREE R-VALUE / ESU R Free: 0.489
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2831 470 4.905 %
Rwork0.225 9112 -
all0.228 --
obs-9582 99.584 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.291 Å2
Baniso -1Baniso -2Baniso -3
1--2.255 Å20 Å20 Å2
2--5.109 Å2-0 Å2
3----2.855 Å2
Refinement stepCycle: LAST / Resolution: 2.85→37.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 25 155 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162980
X-RAY DIFFRACTIONr_angle_refined_deg0.9651.6484170
X-RAY DIFFRACTIONr_angle_other_deg0.3271.5886890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.465516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68410609
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.34910148
X-RAY DIFFRACTIONr_chiral_restr0.0470.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
X-RAY DIFFRACTIONr_nbd_refined0.2240.2695
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22772
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21517
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.235
X-RAY DIFFRACTIONr_nbd_other0.1810.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.214
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.052940
X-RAY DIFFRACTIONr_ncsr_local_group_20.1180.052979
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.053005
X-RAY DIFFRACTIONr_ncsr_local_group_40.0970.053128
X-RAY DIFFRACTIONr_ncsr_local_group_50.130.052898
X-RAY DIFFRACTIONr_ncsr_local_group_60.1210.052941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.114620.05009
12AX-RAY DIFFRACTIONLocal ncs0.114620.05009
23AX-RAY DIFFRACTIONLocal ncs0.117980.0501
24AX-RAY DIFFRACTIONLocal ncs0.117980.0501
35AX-RAY DIFFRACTIONLocal ncs0.113420.0501
36AX-RAY DIFFRACTIONLocal ncs0.113420.0501
47AX-RAY DIFFRACTIONLocal ncs0.097070.0501
48AX-RAY DIFFRACTIONLocal ncs0.097070.0501
59AX-RAY DIFFRACTIONLocal ncs0.129860.05009
510AX-RAY DIFFRACTIONLocal ncs0.129860.05009
611AX-RAY DIFFRACTIONLocal ncs0.121330.0501
612AX-RAY DIFFRACTIONLocal ncs0.121330.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.85-2.9240.407400.3276600.3317020.9150.90899.71510.298
2.924-3.0030.366340.3146230.3176570.8960.9181000.285
3.003-3.090.411330.2996210.3056540.8880.9281000.27
3.09-3.1840.37370.2776070.2836450.8590.93699.8450.238
3.184-3.2880.368340.2785770.2836110.9170.9391000.236
3.288-3.4020.314260.2555730.2575990.9120.951000.22
3.402-3.530.322240.2275640.2315890.9110.96499.83020.196
3.53-3.6720.279290.2525020.2535410.9450.95898.15160.216
3.672-3.8340.236280.25080.2025370.9650.97499.81380.169
3.834-4.0190.204240.234900.2295300.9770.96596.98110.196
4.019-4.2340.262310.1814510.1884820.9520.9771000.158
4.234-4.4870.198200.1774760.1784960.9810.9791000.154
4.487-4.7920.17230.1894040.1884280.9830.97699.76640.157
4.792-5.1690.235170.1834070.1854240.9690.9791000.16
5.169-5.6520.327130.223580.2243720.9220.96799.73120.181
5.652-6.3010.285110.2193630.2213740.9380.9671000.186
6.301-7.2420.231150.1922910.1943060.9530.9751000.162
7.242-8.7890.192170.172630.1712800.9770.981000.154
8.789-12.1050.28990.1632230.1672320.9580.9831000.149
12.105-37.6960.94650.2541510.2651580.0160.95998.73420.246

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