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- PDB-3shf: Crystal structure of the R265S mutant of full-length murine Apaf-1 -

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Basic information

Entry
Database: PDB / ID: 3shf
TitleCrystal structure of the R265S mutant of full-length murine Apaf-1
ComponentsApoptotic peptidase activating factor 1
KeywordsAPOPTOSIS / tandem beta-propeller / cytochrome c / adenine nucleotide / procaspase-9 / cytosol
Function / homology
Function and homology information


Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / regulation of apoptotic DNA fragmentation / apoptosome / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to transforming growth factor beta stimulus / forebrain development / heat shock protein binding ...Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / regulation of apoptotic DNA fragmentation / apoptosome / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to transforming growth factor beta stimulus / forebrain development / heat shock protein binding / cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway / Neutrophil degranulation / response to nutrient / kidney development / neural tube closure / positive regulation of apoptotic signaling pathway / ADP binding / brain development / neuron apoptotic process / cell differentiation / response to hypoxia / 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 / NB-ARC ...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 / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / P-loop containing nucleotide triphosphate hydrolases / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GAMMA-BUTYROLACTONE / Apoptotic protease-activating factor 1 / Apoptotic protease-activating factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsEschenburg, S. / Reubold, T.F.
CitationJournal: Structure / Year: 2011
Title: Crystal structure of full-length Apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis.
Authors: Reubold, T.F. / Wohlgemuth, S. / Eschenburg, S.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptotic peptidase activating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4594
Polymers141,8591
Non-polymers5993
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.880, 111.820, 244.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 141859.234 Da / Num. of mol.: 1 / Mutation: R265S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Sf21 / Gene: Apaf1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2RRK8, UniProt: O88879*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GBL / GAMMA-BUTYROLACTONE / DIHYDROFURAN-2(3H)-ONE


Mass: 86.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.0, 1.4 M sodium malonate, 4% v/v gamma-butyrolactone, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.55→20 Å / Num. all: 24831 / Num. obs: 24831 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.685 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.55-3.80.4434.4437496449999.4
3.8-40.2787.1123414283599.4
4-4.50.14713.3242137510499.7
4.5-50.0822.7326841327699.6
5-60.07723.5730587376299.8
6-80.05134.7324214304199.8
8-100.02564.818514109899.8
10-120.0277.54384950799.8
12-150.0273.74246134298.8
15-200.01974.5145521298.6
200.0267.9490515587.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3sfz

3sfz


Resolution: 3.55→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7638 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3046 987 random
Rwork0.2297 --
all-24831 -
obs-24673 -
Solvent computationBsol: 55.3858 Å2
Displacement parametersBiso max: 176.06 Å2 / Biso mean: 108.4566 Å2 / Biso min: 26.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.712 Å20 Å20 Å2
2--32.441 Å20 Å2
3----35.153 Å2
Refinement stepCycle: LAST / Resolution: 3.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9010 0 39 73 9122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3951.5
X-RAY DIFFRACTIONc_scbond_it1.4392
X-RAY DIFFRACTIONc_mcangle_it2.5542
X-RAY DIFFRACTIONc_scangle_it2.492.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param t
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param t
X-RAY DIFFRACTION3lig.par t

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