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- PDB-7ysx: Crystal structure of PDE4D complexed with licoisoflavone A -

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Basic information

Entry
Database: PDB / ID: 7ysx
TitleCrystal structure of PDE4D complexed with licoisoflavone A
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4D
KeywordsHYDROLASE / PDE4D / complex / licoisoflavone A / Inhibitor
Function / homology
Function and homology information


signaling receptor regulator activity / negative regulation of relaxation of cardiac muscle / negative regulation of heart contraction / 3',5'-cyclic-AMP phosphodiesterase / positive regulation of interleukin-5 production / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / establishment of endothelial barrier / regulation of cardiac muscle cell contraction / negative regulation of cAMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ...signaling receptor regulator activity / negative regulation of relaxation of cardiac muscle / negative regulation of heart contraction / 3',5'-cyclic-AMP phosphodiesterase / positive regulation of interleukin-5 production / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / establishment of endothelial barrier / regulation of cardiac muscle cell contraction / negative regulation of cAMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / positive regulation of heart rate / heterocyclic compound binding / adrenergic receptor signaling pathway / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-serine phosphorylation / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / DARPP-32 events / calcium channel regulator activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / beta-2 adrenergic receptor binding / cAMP binding / cellular response to cAMP / calcium channel complex / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / regulation of heart rate / cAMP-mediated signaling / positive regulation of type II interferon production / T cell receptor signaling pathway / ATPase binding / G alpha (s) signalling events / scaffold protein binding / transmembrane transporter binding / apical plasma membrane / centrosome / perinuclear region of cytoplasm / enzyme binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile.
Similarity search - Domain/homology
Chem-JU3 / 3',5'-cyclic-AMP phosphodiesterase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLiu, J.Y. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Bioactive compounds from Huashi Baidu decoction possess both antiviral and anti-inflammatory effects against COVID-19.
Authors: Xu, H. / Li, S. / Liu, J. / Cheng, J. / Kang, L. / Li, W. / Zhong, Y. / Wei, C. / Fu, L. / Qi, J. / Zhang, Y. / You, M. / Zhou, Z. / Zhang, C. / Su, H. / Yao, S. / Zhou, Z. / Shi, Y. / Deng, ...Authors: Xu, H. / Li, S. / Liu, J. / Cheng, J. / Kang, L. / Li, W. / Zhong, Y. / Wei, C. / Fu, L. / Qi, J. / Zhang, Y. / You, M. / Zhou, Z. / Zhang, C. / Su, H. / Yao, S. / Zhou, Z. / Shi, Y. / Deng, R. / Lv, Q. / Li, F. / Qi, F. / Chen, J. / Zhang, S. / Ma, X. / Xu, Z. / Li, S. / Xu, Y. / Peng, K. / Shi, Y. / Jiang, H. / Gao, G.F. / Huang, L.
History
DepositionAug 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,39113
Polymers80,1932
Non-polymers1,19811
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.479, 80.642, 163.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cAMP-specific 3',5'-cyclic phosphodiesterase 4D / PDE4D / DPDE3 / PDE43


Mass: 40096.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4D, DPDE3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q08499, 3',5'-cyclic-AMP phosphodiesterase

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Non-polymers , 5 types, 237 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-JU3 / 3-[3-(3-methylbut-2-enyl)-2,4-bis(oxidanyl)phenyl]-5,7-bis(oxidanyl)chromen-4-one / Licoisoflavone A


Mass: 354.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 0.2 M MgCl2, 10 % (v/v) Isopropanol, 30 % (v/v) Ethylene glycol, 18 %(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→81.64 Å / Num. obs: 92084 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.024 / Rrim(I) all: 0.082 / Net I/σ(I): 19.5 / Num. measured all: 1004244 / Scaling rejects: 90
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.748.70.981114922132660.7820.3481.0432.6100
5.22-81.6411.10.0343532631700.9990.0110.03654.999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.01 Å81.64 Å
Translation5.01 Å81.64 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
SCALA0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CBQ

7cbq


Resolution: 1.65→36.42 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 4573 4.97 %
Rwork0.1966 87398 -
obs0.1976 91971 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.02 Å2 / Biso mean: 33.2469 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.65→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 76 226 5364
Biso mean--36.7 34.55 -
Num. residues----639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.670.29811440.264928462990
1.67-1.690.27961450.255129033048
1.69-1.710.24081640.247828543018
1.71-1.730.28271570.232128533010
1.73-1.750.27271390.228529243063
1.75-1.780.27191390.223528693008
1.78-1.80.25431780.2228823060
1.8-1.830.23771640.216528443008
1.83-1.860.24311210.211829273048
1.86-1.890.27071280.207428803008
1.89-1.920.22831480.207729183066
1.92-1.960.22821620.202528643026
1.96-1.990.22181450.206228873032
1.99-2.030.21861480.199229063054
2.03-2.080.21831650.200528643029
2.08-2.130.19951520.188329273079
2.13-2.180.21761580.186128703028
2.18-2.240.21361670.188329073074
2.24-2.310.23661580.195829243082
2.31-2.380.23551510.196428833034
2.38-2.470.21181430.188929053048
2.47-2.560.25271320.197329423074
2.56-2.680.2111450.198229273072
2.68-2.820.23071530.194829293082
2.82-30.20591560.200229443100
3-3.230.21551650.209229393104
3.23-3.550.20281380.194829643102
3.55-4.070.21891710.190329743145
4.07-5.120.19071700.174730033173
5.12-36.420.19151670.188631393306
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)
16.80781.87020.24298.8792-1.82395.88820.1220.55150.4222-0.9886-0.02940.2427-0.5078-0.3175-0.07380.32280.05870.01710.2462-0.00280.143210.582612.361912.929
22.2327-0.4821-0.74072.26980.47812.48370.09170.12550.1788-0.1561-0.07340.2302-0.2672-0.2256-0.0240.14840.0222-0.00760.12090.00920.15567.958411.390727.2876
33.6533-1.88310.02772.4998-0.11791.9328-0.0324-0.16510.38730.14120.033-0.2606-0.19350.16840.01440.1389-0.04890.01190.1244-0.01470.156920.913311.344738.3895
41.94881.5956-6.9719.36885.08088.0205-0.0049-0.1722-0.19780.3806-0.03860.25470.1542-0.11290.08960.1155-0.0068-0.01960.15260.02480.11567.74867.683341.4651
51.40870.2307-0.84592.2668-0.29232.9137-0.1141-0.0932-0.2470.2301-0.00530.33950.4799-0.28380.05940.2111-0.05180.04610.16010.00250.27027.2598-6.976333.301
66.11410.22445.31371.75060.70985.6980.03380.3706-0.0692-0.20710.0774-0.2908-0.04580.7326-0.06770.1563-0.00670.07240.23250.00570.200729.46131.524320.4986
79.76785.85284.57493.61833.58414.4370.03960.2202-0.33750.09880.2901-0.4230.25830.6751-0.34210.20940.09320.01840.279-0.00020.365232.5836-7.03923.8764
82.85890.0098-2.22442.2364-0.42126.6714-0.290.2099-0.4054-0.0221-0.13620.16830.8856-0.24680.39060.2641-0.03830.03450.1206-0.03350.243612.8334-11.403219.0905
91.927-0.0098-1.13690.9395-0.07182.5159-0.3292-0.85660.02570.28510.4942-0.44750.51971.4322-0.13540.3640.3398-0.08890.7944-0.10560.305535.57634.731469.3563
103.0573-0.60150.18862.85370.35914.2116-0.07330.07220.2924-0.05170.2156-0.2797-0.10110.2794-0.09860.130.00120.01680.1603-0.03370.153526.197210.484454.1186
110.9141-0.23080.40394.2256-0.73240.6581-0.74820.2206-0.46160.31010.39370.04931.16390.01520.27970.67830.09650.14590.2297-0.04420.268824.6407-8.176857.7639
123.3424-0.7986-2.1091.46380.22043.0566-0.0461-0.13610.1706-0.21780.0021-0.15420.33620.03590.03180.42560.14880.03050.24360.00580.203218.91225.251169.0141
132.6858-2.74711.93742.1696-6.41727.23350.28420.60310.1977-0.075-0.0310.4512-0.0012-1.1279-0.2210.39090.12530.03820.47840.05640.31136.1719.326671.5797
140.733-0.7323-0.62411.60941.43381.5187-0.4671-0.7277-0.1683-0.0412-0.12760.03492.05590.15830.31171.18320.30030.2060.06350.25310.202216.6331-6.498277.9462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 88 through 116 )A88 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 199 )A117 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 253 )A200 - 253
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 271 )A254 - 271
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 325 )A272 - 325
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 349 )A326 - 349
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 375 )A350 - 375
8X-RAY DIFFRACTION8chain 'A' and (resid 376 through 410 )A376 - 410
9X-RAY DIFFRACTION9chain 'B' and (resid 88 through 199 )B88 - 199
10X-RAY DIFFRACTION10chain 'B' and (resid 200 through 253 )B200 - 253
11X-RAY DIFFRACTION11chain 'B' and (resid 254 through 302 )B254 - 302
12X-RAY DIFFRACTION12chain 'B' and (resid 303 through 350 )B303 - 350
13X-RAY DIFFRACTION13chain 'B' and (resid 351 through 375 )B351 - 375
14X-RAY DIFFRACTION14chain 'B' and (resid 376 through 410 )B376 - 410

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