[English] 日本語
Yorodumi
- PDB-11ap: Crystal structure of mouse DXO in complex with the UDP-N-acetylgl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11ap
TitleCrystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap
ComponentsDecapping and exoribonuclease protein
KeywordsRNA BINDING PROTEIN / Noncanonical RNA cap / DXO/Rai1 family of enzymes UDP-glucose (UDP-Glc) and UDP-N-acetylglucosamine (UDP-GlcNAc) / DXO
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
: / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUllah, N. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Decapping and exoribonuclease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6784
Polymers40,9611
Non-polymers7173
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.880, 87.990, 53.580
Angle α, β, γ (deg.)90.000, 113.032, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
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: 40961.172 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 BL21(DE3) (bacteria)
References: UniProt: O70348, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 21-25% (w/v) PEG 3350 and 0.1 M Tris (pH 6.8).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.8→49.5 Å / Num. obs: 38997 / % possible obs: 98.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.55 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 6193 / CC1/2: 0.722

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.31 Å / SU ML: 0.1879 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2064 1963 5.05 %
Rwork0.1648 36926 -
obs0.167 38889 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 41 423 3353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583044
X-RAY DIFFRACTIONf_angle_d0.85984160
X-RAY DIFFRACTIONf_chiral_restr0.0523419
X-RAY DIFFRACTIONf_plane_restr0.0083548
X-RAY DIFFRACTIONf_dihedral_angle_d14.26951170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.31461370.27052658X-RAY DIFFRACTION98.24
1.85-1.890.24591410.21972575X-RAY DIFFRACTION97.7
1.89-1.950.23761330.19822562X-RAY DIFFRACTION96.8
1.95-2.010.23521430.19812662X-RAY DIFFRACTION99.22
2.01-2.090.2141270.17062635X-RAY DIFFRACTION99.32
2.09-2.170.22381470.16722646X-RAY DIFFRACTION99.01
2.17-2.270.22731450.1662635X-RAY DIFFRACTION98.9
2.27-2.390.22251450.16552657X-RAY DIFFRACTION98.94
2.39-2.540.21031340.16952639X-RAY DIFFRACTION99.39
2.54-2.730.22331030.18462620X-RAY DIFFRACTION96.59
2.73-3.010.2182070.1732598X-RAY DIFFRACTION99.15
3.01-3.440.21051600.16782645X-RAY DIFFRACTION99.47
3.44-4.340.202480.1312762X-RAY DIFFRACTION99.22
4.34-49.310.15791930.14482632X-RAY DIFFRACTION97.85

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more