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- PDB-4ikg: Crystal structure of cell death-inducing DFFA-like effector c -

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Basic information

Entry
Database: PDB / ID: 4ikg
TitleCrystal structure of cell death-inducing DFFA-like effector c
ComponentsCell death activator CIDE-3
KeywordsAPOPTOSIS / Fsp27 / cell death
Function / homology
Function and homology information


Lipid particle organization / lipid droplet fusion / lipid transfer activity / negative regulation of triglyceride metabolic process / phosphatidic acid binding / lipid storage / execution phase of apoptosis / phosphatidylserine binding / negative regulation of lipid catabolic process / lipid droplet ...Lipid particle organization / lipid droplet fusion / lipid transfer activity / negative regulation of triglyceride metabolic process / phosphatidic acid binding / lipid storage / execution phase of apoptosis / phosphatidylserine binding / negative regulation of lipid catabolic process / lipid droplet / phosphatidylinositol binding / molecular condensate scaffold activity / apoptotic process / endoplasmic reticulum / nucleus / cytosol
Similarity search - Function
CIDE-N domain / CIDE-N domain / CIDE-N domain profile. / Domains present in proteins implicated in post-mortem DNA fragmentation / Ubiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Lipid transferase CIDEC
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9318 Å
AuthorsYang, M. / Gao, J.
CitationJournal: Nat Commun / Year: 2013
Title: Perilipin1 promotes unilocular lipid droplet formation through the activation of Fsp27 in adipocytes.
Authors: Sun, Z. / Gong, J. / Wu, H. / Xu, W. / Wu, L. / Xu, D. / Gao, J. / Wu, J.W. / Yang, H. / Yang, M. / Li, P.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell death activator CIDE-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8096
Polymers9,1751
Non-polymers6355
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.615, 61.615, 44.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell death activator CIDE-3 / Cell death-inducing DFFA-like effector protein C / Fat-specific protein FSP27


Mass: 9174.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cidec, Fsp27 / Production host: Escherichia coli (E. coli) / References: UniProt: P56198
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1M TRIS hydrochloride pH8.5, 28% polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9318→53.51 Å / Num. all: 13577 / Num. obs: 12963

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Processing

Software
NameVersionClassification
HKL-2000data collection
DMmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9318→26.68 Å / SU ML: 0.24 / σ(F): 1.32 / Phase error: 46.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3056 595 4.74 %
Rwork0.2924 --
obs0.2931 12552 87.63 %
all-13147 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.938 Å2-0 Å20 Å2
2---7.938 Å2-0 Å2
3---15.876 Å2
Refinement stepCycle: LAST / Resolution: 1.9318→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms623 0 5 28 656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007666
X-RAY DIFFRACTIONf_angle_d1.128897
X-RAY DIFFRACTIONf_dihedral_angle_d18.182264
X-RAY DIFFRACTIONf_chiral_restr0.083101
X-RAY DIFFRACTIONf_plane_restr0.003114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9318-2.12610.3881960.36911793X-RAY DIFFRACTION53
2.1261-2.43360.38141460.38273355X-RAY DIFFRACTION98
2.4336-3.06530.31561550.34053434X-RAY DIFFRACTION100
3.0653-26.68260.28831980.2553375X-RAY DIFFRACTION100
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)
13.63390.90740.55275.65311.47420.60811.0407-0.2328-0.31950.2607-0.51290.78730.1307-0.0857-0.02870.45180.0415-0.14590.4597-0.10910.5025-9.326113.8139-0.6235
20.6639-1.10431.52812.7556-4.35528.3161-0.52170.68150.9491-0.9523-0.3630.5682-0.95880.62080.64090.8092-0.067-0.36820.35140.190.4867-5.726919.6357-16.8318
39.90424.26872.12624.28390.27579.0515-1.4302-0.5853.07950.3032-0.49391.6657-2.07-0.71061.74770.5530.1033-0.5550.246-0.15540.8298-10.139722.2153-8.0259
40.8178-0.0955-0.08556.1331-2.11630.94910.17321.00630.5344-0.9354-0.1831-2.2715-0.11260.36890.07751.3229-0.0036-1.04770.2391-0.04691.6299-10.882130.2099-13.3677
58.81611.1901-0.7780.4444-0.14964.4993-0.5236-0.09663.2443-0.8930.35280.1487-1.1323-0.6040.42120.57610.1068-0.39160.3036-0.01490.7893-15.025415.63-16.269
62.44040.8611.35871.23230.18381.4528-0.6403-0.26550.9794-0.31630.04230.4307-0.4264-0.26920.44730.31460.0521-0.06340.398-0.08660.4318-13.86810.0897-7.7474
72.038-2.62977.56722.2388-2.21945.453-1.0297-0.69232.1116-0.94760.0083-0.0273-1.5073-0.6440.62231.03680.0198-0.48490.19580.28160.6624-13.130518.4869-20.4629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 41:45)
2X-RAY DIFFRACTION2(chain A and resid 46:52)
3X-RAY DIFFRACTION3(chain A and resid 53:72)
4X-RAY DIFFRACTION4(chain A and resid 73:78)
5X-RAY DIFFRACTION5(chain A and resid 79:91)
6X-RAY DIFFRACTION6(chain A and resid 92:106)
7X-RAY DIFFRACTION7(chain A and resid 107:118)

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