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- PDB-10yz: Crystal structure of mouse DXO in complex with pGGGUU RNA and two... -

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Basic information

Entry
Database: PDB / ID: 10yz
TitleCrystal structure of mouse DXO in complex with pGGGUU RNA and two magnesium ions
Components
  • Decapping and exoribonuclease protein
  • RNA (5'-R(GP*GP*GP*UP*U)-3')
KeywordsHYDROLASE/RNA / dxo / RNA / decapping / exoribonuclease / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / NAD-cap decapping / nuclear mRNA surveillance / 5'-3' exonuclease activity / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / NAD-cap decapping / nuclear mRNA surveillance / 5'-3' exonuclease activity / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / mRNA binding / magnesium ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
RNA / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDoamekpor, S.K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Crystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap and molecular mechanism for the decapping reactions.
Authors: Ullah, N. / Doamekpor, S.K. / Tong, L.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decapping and exoribonuclease protein
C: RNA (5'-R(GP*GP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9884
Polymers46,9392
Non-polymers492
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-30 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.365, 87.999, 50.156
Angle α, β, γ (deg.)90.00, 114.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Decapping and exoribonuclease protein / DXO / 5'-3' exoribonuclease DXO / Dom-3 homolog Z / NAD-capped RNA hydrolase DXO / DeNADding enzyme DXO


Mass: 45336.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dxo, Dom3z, Ng6 / Production host: Escherichia coli (E. coli)
References: UniProt: O70348, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(GP*GP*GP*UP*U)-3')


Mass: 1602.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: pGGGUU RNA / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→200 Å / Num. obs: 90199 / % possible obs: 94.8 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.017 / Rrim(I) all: 0.023 / Net I/σ(I): 12.12
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.70.12328830.9330.1741
1.7-1.820.07727550.9730.1081
1.82-1.960.05628150.9920.0791
1.96-2.150.03724940.9950.0521
2.15-2.40.02520760.9980.0361
2.4-2.770.02316660.9980.0321
2.77-3.390.01713400.9980.0241
3.39-4.780.0158920.9990.0211
4.78-2000.0125370.9990.0171

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.23 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 2005 4.22 %
Rwork0.1834 --
obs0.1845 47559 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 74 2 323 3288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063121
X-RAY DIFFRACTIONf_angle_d0.8594284
X-RAY DIFFRACTIONf_dihedral_angle_d14.6611192
X-RAY DIFFRACTIONf_chiral_restr0.052432
X-RAY DIFFRACTIONf_plane_restr0.01552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.331330.29593158X-RAY DIFFRACTION97
1.64-1.690.33311440.27833270X-RAY DIFFRACTION99
1.69-1.740.27451490.24663223X-RAY DIFFRACTION98
1.74-1.790.25621390.20853217X-RAY DIFFRACTION98
1.79-1.860.22391490.19443267X-RAY DIFFRACTION100
1.86-1.930.23351300.19943280X-RAY DIFFRACTION99
1.93-2.020.23051520.19673257X-RAY DIFFRACTION100
2.02-2.120.19691430.19283254X-RAY DIFFRACTION99
2.12-2.260.20261440.18113272X-RAY DIFFRACTION99
2.26-2.430.23881460.18883265X-RAY DIFFRACTION99
2.43-2.680.2321420.19943243X-RAY DIFFRACTION99
2.68-3.060.21341440.18273303X-RAY DIFFRACTION100
3.06-3.860.18041410.1633267X-RAY DIFFRACTION98
3.86-42.230.18771490.15863278X-RAY DIFFRACTION98

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