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- PDB-6iie: Crystal structure of human diacylglycerol kinase alpha EF-hand do... -

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Basic information

Entry
Database: PDB / ID: 6iie
TitleCrystal structure of human diacylglycerol kinase alpha EF-hand domains bound to Ca2+
ComponentsDiacylglycerol kinase alpha
KeywordsTRANSFERASE / Lipid kinase / diaclyglycerol / diacylglycerol kinase / EF-hand / calcium binding proteins / ligand mimic helix / dimer formation
Function / homology
Function and homology information


alkylglycerol kinase / alkylglycerol kinase activity / lipid phosphorylation / glycerolipid metabolic process / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / Effects of PIP2 hydrolysis / : ...alkylglycerol kinase / alkylglycerol kinase activity / lipid phosphorylation / glycerolipid metabolic process / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / Effects of PIP2 hydrolysis / : / platelet activation / phospholipid binding / kinase activity / intracellular signal transduction / lipid binding / calcium ion binding / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Diacylglycerol kinase type I, N-terminal / DGK type I, N-terminal domain superfamily / : / Diacylglycerol kinase N-terminus / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain ...Diacylglycerol kinase type I, N-terminal / DGK type I, N-terminal domain superfamily / : / Diacylglycerol kinase N-terminus / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Diacylglycerol kinase alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.142 Å
AuthorsTakahashi, D. / Suzuki, K. / Sakamoto, T. / Iwamoto, T. / Murata, T. / Sakane, F.
CitationJournal: Protein Sci. / Year: 2019
Title: Crystal structure and calcium-induced conformational changes of diacylglycerol kinase alpha EF-hand domains.
Authors: Takahashi, D. / Suzuki, K. / Sakamoto, T. / Iwamoto, T. / Murata, T. / Sakane, F.
History
DepositionOct 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Diacylglycerol kinase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2697
Polymers10,6161
Non-polymers6536
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area5640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.190, 58.190, 61.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Diacylglycerol kinase alpha / DAG kinase alpha / 80 kDa diacylglycerol kinase / Diglyceride kinase alpha / DGK-alpha


Mass: 10616.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DGKA, DAGK, DAGK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P23743, diacylglycerol kinase (ATP)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 1.0 M succinic acid, 2 % PEG monomethyl ether 2000, 10 % glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001Y
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
Detector
TypeIDDetectorDate
DECTRIS EIGER X 4M1PIXELNov 27, 2017
DECTRIS EIGER X 4M2PIXELMar 6, 2018
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection

Biso Wilson estimate: 44.49 Å2 / Entry-ID: 6IIE

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRsym valueDiffraction-IDNet I/σ(I)
2.142-50687699.99.70.9980.0830.0280.083115.13
2.75-50569398.534.40.9990.1480.1490.148215.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.142-2.279.880.6612.9110790.8810.69899.2
2.27-2.4310.0650.4344.8410260.9520.457100
2.43-2.629.9360.2977.369490.9690.313100
2.62-2.879.8280.18511.338840.990.196100
2.87-3.219.230.11516.428140.9950.122100
3.21-3.78.8870.07424.347150.9970.078100
3.7-4.529.8240.0633.476200.9980.063100
4.52-6.359.7690.05634.134890.9980.059100
6.35-38.888.6970.05535.823000.9960.05999.7
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: cryo loop / Support base: goniometer
Serial crystallography data reductionFrames indexed: 14400 / Frames total: 14400

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.142→38.882 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.94
RfactorNum. reflection% reflection
Rfree0.2376 344 5 %
Rwork0.1854 --
obs0.1879 6875 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.6 Å2 / Biso mean: 60.056 Å2 / Biso min: 30.72 Å2
Refinement stepCycle: final / Resolution: 2.142→38.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 40 9 743
Biso mean--73.76 48.26 -
Num. residues----87
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013746
X-RAY DIFFRACTIONf_angle_d1.315998
X-RAY DIFFRACTIONf_chiral_restr0.069111
X-RAY DIFFRACTIONf_plane_restr0.007124
X-RAY DIFFRACTIONf_dihedral_angle_d8.402628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1425-2.69920.26791680.217231963364
2.6992-38.88830.22961760.177833353511
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)
12.2258-2.40470.84329.0608-2.91082.8931-0.01190.27770.83840.19150.2199-0.3532-1.0818-0.0083-0.12030.551-0.05170.02440.367-0.0270.3979-23.897317.190910.581
22.1456-0.07371.57299.3758-3.46842.3746-0.2792-0.2886-0.44580.58290.347-0.8090.40270.2778-0.37150.46190.0002-0.0710.4582-0.05850.4492-19.71296.00214.5531
34.5147-2.7212.97078.1316-3.17274.7737-0.20390.3992-0.8273-0.78190.77320.50010.4129-0.3873-0.7120.5409-0.1256-0.02380.4153-0.00180.352-27.44245.84530.5416
41.7789-2.16170.87488.771-0.12767.60320.39312.5222-1.0316-3.4813-0.34050.29230.8019-1.3995-0.53891.2445-0.2455-0.05821.0622-0.00980.7999-31.00628.2757-12.3202
55.9426-0.3536.00412.97760.0036.1027-0.37130.98540.1359-1.3095-0.0838-0.86180.50350.84090.40670.7991-0.03430.29640.5821-0.0020.6091-18.17617.5123-4.3943
63.36692.81261.46532.40051.97398.7413-0.31920.02220.2059-0.2772-0.3795-2.52550.49812.94590.90450.53230.04430.14590.86550.19481.0935-9.84858.98245.825
78.3183-3.60656.30776.8331-5.2899.8166-0.08590.8357-0.0870.6607-0.2292-2.3341-0.69481.03570.69030.4185-0.0909-0.060.3854-0.03970.7411-15.687116.50756.8005
85.74512.216.43465.82142.35917.202-1.1311.64211.01660.35150.6498-1.8411-0.48290.88420.70790.5503-0.18660.12090.46050.13620.6182-18.044420.2544-1.0998
95.3814-4.03575.71875.5747-4.34256.4722-0.4071-0.46470.7901-0.56670.8452-0.0299-0.587-0.959-0.23680.3978-0.13370.03910.48120.02790.3664-27.824517.15230.8446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 122 )A111 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 131 )A123 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 148 )A132 - 148
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 155 )A149 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 167 )A156 - 167
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 176 )A168 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 184 )A177 - 184
8X-RAY DIFFRACTION8chain 'A' and (resid 185 through 189 )A185 - 189
9X-RAY DIFFRACTION9chain 'A' and (resid 190 through 197 )A190 - 197

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