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- PDB-9sq2: H/D exchanged human SMUG1 in complex with deuterated uracil -

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Basic information

Entry
Database: PDB / ID: 9sq2
TitleH/D exchanged human SMUG1 in complex with deuterated uracil
ComponentsSingle-strand selective monofunctional uracil DNA glycosylase
KeywordsHYDROLASE / H/D exchange / X/N joint refinement / SMUG1 / DNA glycosylase / deuterated uracil
Function / homology
Function and homology information


single-strand selective uracil DNA N-glycosylase activity / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair ...single-strand selective uracil DNA N-glycosylase activity / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair / fibrillar center / nucleolus / DNA binding / nucleoplasm / identical protein binding
Similarity search - Function
Single-strand selective monofunctional uracil DNA glycosylase / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
URACIL / Single-strand selective monofunctional uracil DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLudaescher, J.M. / Scaletti Hutchinson, E. / Aggarwal, S. / Gajdos, L. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Cancerfonden Sweden
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for uracil removal from DNA by human SMUG1.
Authors: Ludascher, J.M. / Scaletti Hutchinson, E. / Vila-Julia, G. / Jemth, A.S. / Shahid, S. / Wiita, E. / Cabeza de Vaca, I. / Pach, S. / Gajdos, L. / Aggarwal, S. / Walse, E. / Mortusewicz, O. / ...Authors: Ludascher, J.M. / Scaletti Hutchinson, E. / Vila-Julia, G. / Jemth, A.S. / Shahid, S. / Wiita, E. / Cabeza de Vaca, I. / Pach, S. / Gajdos, L. / Aggarwal, S. / Walse, E. / Mortusewicz, O. / Helleday, T. / Carlsson, J. / Stenmark, P.
History
DepositionSep 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-strand selective monofunctional uracil DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6493
Polymers27,3741
Non-polymers2752
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint3 kcal/mol
Surface area11010 Å2
Unit cell
Length a, b, c (Å)49.859, 61.136, 93.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Single-strand selective monofunctional uracil DNA glycosylase


Mass: 27373.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMUG1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53HV7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Buffer System 3 pH 8.4, 50 % (v/v) P500MME_P20K, 0.12 M Alcohols Mix (Morpheus Screen, Molecular Dimensions), 30% D2O.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
22921N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM0710.9795
NUCLEAR REACTORILL LADI III22.8-3.8
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 5, 2025
LADI III2IMAGE PLATEMay 20, 2025
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
22.81
33.81
Reflection

Entry-ID: 9SQ2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Diffraction-IDNet I/σ(I)
1.54-46.934272999.512.80.999117.8
2.3-30.361169090.66.70.99428.7
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
1.54-1.61.439690.4861
2.3-2.422.215230.5912

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Processing

Refinement

Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
1.54-29.83X-RAY DIFFRACTION31.480.1790.157521334052942662599.491
2.31-30.36NEUTRON DIFFRACTION0.27490.2395116035.010.8852
Refinement stepCycle: LAST / Resolution: 1.54→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 19 109 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01582063
X-RAY DIFFRACTIONf_angle_d1.37032815
X-RAY DIFFRACTIONf_chiral_restr0.0722297
X-RAY DIFFRACTIONf_plane_restr0.0152478
X-RAY DIFFRACTIONf_dihedral_angle_d16.5411788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.30171320.29312510X-RAY DIFFRACTION93.65
1.58-1.620.26831400.26032661X-RAY DIFFRACTION99.93
1.62-1.660.27231410.22662663X-RAY DIFFRACTION99.86
1.66-1.710.22491420.20692703X-RAY DIFFRACTION99.93
1.71-1.770.21921400.19212663X-RAY DIFFRACTION99.93
1.77-1.830.21321420.17932705X-RAY DIFFRACTION100
1.83-1.90.22451410.17282677X-RAY DIFFRACTION99.82
1.9-1.990.19951410.16652687X-RAY DIFFRACTION99.89
1.99-2.10.15761410.15442685X-RAY DIFFRACTION100
2.1-2.230.16431430.15362703X-RAY DIFFRACTION100
2.23-2.40.18791450.15262739X-RAY DIFFRACTION99.93
2.4-2.640.18761430.162716X-RAY DIFFRACTION99.9
2.64-3.020.18891440.16392741X-RAY DIFFRACTION99.83
3.02-3.810.17681460.15242776X-RAY DIFFRACTION99.76
3.81-29.830.14141520.13052900X-RAY DIFFRACTION99.87

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