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- PDB-1tb7: Catalytic Domain Of Human Phosphodiesterase 4D In Complex With AMP -

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Basic information

Entry
Database: PDB / ID: 1tb7
TitleCatalytic Domain Of Human Phosphodiesterase 4D In Complex With AMP
ComponentscAMP-specific 3',5'-cyclic phosphodiesterase 4D
KeywordsHYDROLASE / PDE4D
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 / regulation of cardiac muscle cell contraction / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / beta-2 adrenergic receptor binding / 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 / regulation of cardiac muscle cell contraction / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / beta-2 adrenergic receptor binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / heterocyclic compound binding / adrenergic receptor signaling pathway / voltage-gated calcium channel complex / regulation of cell communication by electrical coupling involved in cardiac conduction / cAMP catabolic process / calcium channel regulator activity / cAMP-mediated signaling / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / negative regulation of peptidyl-serine phosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cAMP binding / cellular response to cAMP / cellular response to epinephrine stimulus / calcium channel complex / positive regulation of interleukin-2 production / regulation of heart rate / positive regulation of type II interferon production / ATPase binding / T cell receptor signaling pathway / G alpha (s) signalling events / scaffold protein binding / transmembrane transporter binding / apical plasma membrane / centrosome / perinuclear region of cytoplasm / enzyme binding / signal transduction / membrane / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 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. ...Phosphodiesterase 4 upstream conserved regions (UCR) / Phosphodiesterase 4 upstream conserved regions (UCR) / Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 3',5'-cyclic-AMP phosphodiesterase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZhang, K.Y.J. / Card, G.L. / Suzuki, Y. / Artis, D.R. / Fong, D. / Gillette, S. / Hsieh, D. / Neiman, J. / West, B.L. / Zhang, C. ...Zhang, K.Y.J. / Card, G.L. / Suzuki, Y. / Artis, D.R. / Fong, D. / Gillette, S. / Hsieh, D. / Neiman, J. / West, B.L. / Zhang, C. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Bollag, G.
CitationJournal: Mol.Cell / Year: 2004
Title: A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases
Authors: Zhang, K.Y.J. / Card, G.L. / Suzuki, Y. / Artis, D.R. / Fong, D. / Gillette, S. / Hsieh, D. / Neiman, J. / West, B.L. / Zhang, C. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Bollag, G.
History
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,24736
Polymers76,4152
Non-polymers2,83234
Water6,467359
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A: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,79519
Polymers38,2071
Non-polymers1,58818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,45117
Polymers38,2071
Non-polymers1,24416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.316, 78.958, 164.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is one monomer.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38207.273 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus(RIL)
References: UniProt: Q08499, 3',5'-cyclic-nucleotide phosphodiesterase

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Non-polymers , 6 types, 393 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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3000, ethylene glycol, isopropanol, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.63→81.65 Å / Num. all: 86294 / Num. obs: 86294 / % possible obs: 91.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9
Reflection shellResolution: 1.63→1.672 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.65 / Num. unique all: 5428 / % possible all: 76.4

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
Blu-Icedata collection
ELVESdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→81.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.761 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19185 4527 5 %RANDOM
Rwork0.17927 ---
all0.17991 86294 --
obs0.17991 86294 91.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.999 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.085 Å0.093 Å
Refinement stepCycle: LAST / Resolution: 1.63→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 177 359 5782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215532
X-RAY DIFFRACTIONr_bond_other_d0.0020.024878
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.967460
X-RAY DIFFRACTIONr_angle_other_deg0.805311385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8085644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025925
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021017
X-RAY DIFFRACTIONr_nbd_refined0.2120.21332
X-RAY DIFFRACTIONr_nbd_other0.2260.25500
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.22903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3991.53243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79425295
X-RAY DIFFRACTIONr_scbond_it1.48932289
X-RAY DIFFRACTIONr_scangle_it2.5114.52165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 278 -
Rwork0.303 5150 -
obs-5428 76.4 %
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)
10.4223-0.0784-0.09020.86220.37831.6237-0.0031-0.0167-0.04620.012-0.01970.07590.0158-0.07190.02280.0045-0.00370.01760.04720.01240.122114.6973.42227.915
20.7619-0.1873-0.63040.79050.06621.7447-0.0832-0.08320.0080.04480.053-0.08370.11930.08950.03020.0660.0267-0.00410.0494-0.01130.128526.9152.05266.896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA87 - 4116 - 330
2X-RAY DIFFRACTION2BB86 - 4115 - 330

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