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- PDB-6jx6: Tetrameric form of Smac -

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Basic information

Entry
Database: PDB / ID: 6jx6
TitleTetrameric form of Smac
ComponentsDiablo homolog, mitochondrial
KeywordsAPOPTOSIS / Smac
Function / homology
Function and homology information


: / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway ...: / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway / : / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / neuron apoptotic process / positive regulation of apoptotic process / apoptotic process / mitochondrion / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsSivaraman, J. / Singh, S. / Ng, J. / Nayak, D.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R-154-000-B03-112 Singapore
Ministry of Education (Singapore)R154-000-A72-114 Singapore
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural insights into a HECT-type E3 ligase AREL1 and its ubiquitination activitiesin vitro.
Authors: Singh, S. / Ng, J. / Nayak, D. / Sivaraman, J.
History
DepositionApr 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diablo homolog, mitochondrial
B: Diablo homolog, mitochondrial
C: Diablo homolog, mitochondrial
D: Diablo homolog, mitochondrial


Theoretical massNumber of molelcules
Total (without water)83,1484
Polymers83,1484
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area31820 Å2
Unit cell
Length a, b, c (Å)82.195, 85.403, 114.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Diablo homolog, mitochondrial / Direct IAP-binding protein with low pI / Second mitochondria-derived activator of caspase / Smac


Mass: 20787.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIABLO, SMAC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR28

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 296 K / Method: vapor diffusion / Details: 200mM Potassium Phosphate Monobasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→47.6 Å / Num. obs: 19689 / % possible obs: 96.63 % / Redundancy: 10.5 % / Biso Wilson estimate: 65.57 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.045 / Net I/σ(I): 22.5
Reflection shellResolution: 2.805→2.905 Å / Num. unique obs: 1880 / CC1/2: 0.906 / Rpim(I) all: 0.202

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G73

1g73


Resolution: 2.805→47.6 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1014 5.15 %
Rwork0.2162 --
obs0.2186 19688 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.805→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 0 0 4638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054739
X-RAY DIFFRACTIONf_angle_d0.8876414
X-RAY DIFFRACTIONf_dihedral_angle_d6.1252876
X-RAY DIFFRACTIONf_chiral_restr0.043768
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.805-2.95290.3181460.25342570X-RAY DIFFRACTION95
2.9529-3.13790.30481540.22722651X-RAY DIFFRACTION99
3.1379-3.38010.28241370.21622724X-RAY DIFFRACTION99
3.3801-3.72010.30371430.22042694X-RAY DIFFRACTION98
3.7201-4.25810.24171560.20992712X-RAY DIFFRACTION99
4.2581-5.36360.26421470.20562707X-RAY DIFFRACTION97
5.3636-47.60680.23241310.21662616X-RAY DIFFRACTION89

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