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- PDB-4qeb: Dcps in complex with covalent inhibitor targeting Tyrosine -

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Basic information

Entry
Database: PDB / ID: 4qeb
TitleDcps in complex with covalent inhibitor targeting Tyrosine
Componentsm7GpppX diphosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Decapping scavenger enzyme / residual cap structure cleavage / mRNA degradation / 3'->5' exosome-mediated mRNA decay pathway / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like ...mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like / HIT family, subunit A / HIT-like superfamily / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-31G / PHOSPHATE ION / m7GpppX diphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLiu, S.
CitationJournal: To be Published
Title: Human Dcps in complex with covalent inhibitor
Authors: Liu, S.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / 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 / _software.name / _struct_conn.pdbx_leaving_atom_flag / _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: m7GpppX diphosphatase
B: m7GpppX diphosphatase
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,0819
Polymers154,3544
Non-polymers7265
Water0
1
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8086
Polymers77,1772
Non-polymers6314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-60 kcal/mol
Surface area25480 Å2
MethodPISA
2
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2723
Polymers77,1772
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-46 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.250, 105.230, 139.960
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
m7GpppX diphosphatase / / DCS-1 / Decapping scavenger enzyme / Hint-related 7meGMP-directed hydrolase / Histidine triad ...DCS-1 / Decapping scavenger enzyme / Hint-related 7meGMP-directed hydrolase / Histidine triad nucleotide-binding protein 5 / Histidine triad protein member 5 / HINT-5 / Scavenger mRNA-decapping enzyme DcpS


Mass: 38588.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCPS, DCS1, HINT5, HSPC015 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96C86, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-31G / 3-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid


Mass: 346.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O4S

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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: 49.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1:1 protein (4 mg/mL in 25 mM NaCl, 20 mM Tris-HCl, pH 8.0, 1 mM TCEP) to precipitant (23-25% PEG3350, 0.1 M potassium phosphate monobasic, 0.05 M sodium chloride, 26% glycerol, crystals ...Details: 1:1 protein (4 mg/mL in 25 mM NaCl, 20 mM Tris-HCl, pH 8.0, 1 mM TCEP) to precipitant (23-25% PEG3350, 0.1 M potassium phosphate monobasic, 0.05 M sodium chloride, 26% glycerol, crystals soaked in 1 mM inhibitor overnight, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9997 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99971
211
ReflectionResolution: 3.2→82.03 Å / Num. obs: 23629 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 77.55 Å2 / Rmerge(I) obs: 0.317 / Net I/σ(I): 3.3

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Processing

Software
NameVersionClassification
Jdirectdata collection
MOLREPphasing
BUSTER2.11.5refinement
autoPROCdata scaling
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XMM

1xmm


Resolution: 3.21→33.89 Å / Cor.coef. Fo:Fc: 0.9182 / Cor.coef. Fo:Fc free: 0.8556 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.622
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1069 5.12 %RANDOM
Rwork0.2107 ---
obs0.214 20868 83.25 %-
Displacement parametersBiso mean: 105.62 Å2
Baniso -1Baniso -2Baniso -3
1-6.163 Å20 Å20 Å2
2--1.1579 Å20 Å2
3----7.3208 Å2
Refine analyzeLuzzati coordinate error obs: 0.851 Å
Refinement stepCycle: LAST / Resolution: 3.21→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 43 0 9604
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3471SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes269HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1430HARMONIC5
X-RAY DIFFRACTIONt_it9839HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1219SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10955SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9839HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg13357HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion23.03
LS refinement shellResolution: 3.21→3.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3511 87 5.57 %
Rwork0.2509 1475 -
all0.2565 1562 -
obs--83.25 %
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)
12.70320.1319-0.28533.47840.2711.38510.00520.4722-0.3044-0.40270.0432-0.3149-0.1093-0.0989-0.0484-0.30650.02820.00560.30150.10270.244134.703240.51824.3861
25.99350.05460.61452.5943-1.20590.85750.1074-0.0462-0.45050.21710.1084-0.12150.0243-0.2145-0.2158-0.41610.0215-0.00320.10010.04360.335146.175523.593241.6582
36.72590.93730.61232.0886-0.7141.23160.10720.37050.5821-0.12560.08-0.0374-0.1911-0.0021-0.1873-0.5111-0.01910.02960.4239-0.1360.486596.601432.719626.7681
47.9865-2.6645-1.63953.15970.07332.0773-0.1019-0.32240.13190.28850.2294-0.26390.0543-0.0599-0.1275-0.455-0.0335-0.02940.4167-0.080.500685.258416.208144.3794
50.711-0.82170.95834.554-0.23731.50680.09870.5527-0.2695-0.51030.09120.0850.4770.0375-0.18990.3387-0.06230.30480.9652-0.26091.251641.193718.96467.0344
602.5694-0.8113.49530.66941.86030.0399-0.41820.54140.44370.29080.094-0.17980.3245-0.33070.22640.0446-0.41060.7899-0.28231.196291.910338.155460.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|146 - A|336 }A146 - 336
2X-RAY DIFFRACTION2{ B|146 - B|336 }B146 - 336
3X-RAY DIFFRACTION3{ C|146 - C|336 }C146 - 336
4X-RAY DIFFRACTION4{ D|146 - D|336 }D146 - 336
5X-RAY DIFFRACTION5{ A|40 - A|145 B|40 - B|145 }A40 - 145
6X-RAY DIFFRACTION5{ A|40 - A|145 B|40 - B|145 }B40 - 145
7X-RAY DIFFRACTION6{ C|39 - C|145 D|40 - D|145 }C39 - 145
8X-RAY DIFFRACTION6{ C|39 - C|145 D|40 - D|145 }D40 - 145

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