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- PDB-9gm2: Human SMUG1 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 9gm2
TitleHuman SMUG1 in complex with DNA
Components
  • DNA (5'-D(P*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*GP*AP*CP*T*ORP*AP*CP*GP*GP*G)-3')
  • Single-strand selective monofunctional uracil DNA glycosylase
KeywordsHYDROLASE / SMUG1 / AP site / DNA
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
DNA / DNA (> 10) / Single-strand selective monofunctional uracil DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLudaescher, J.M. / Scaletti Hutchinson, E. / 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
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 17, 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
B: Single-strand selective monofunctional uracil DNA glycosylase
C: Single-strand selective monofunctional uracil DNA glycosylase
D: Single-strand selective monofunctional uracil DNA glycosylase
E: DNA (5'-D(P*CP*GP*GP*AP*CP*T*ORP*AP*CP*GP*GP*G)-3')
F: DNA (5'-D(P*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3')
G: DNA (5'-D(P*CP*GP*GP*AP*CP*T*ORP*AP*CP*GP*GP*G)-3')
H: DNA (5'-D(P*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)124,3138
Polymers124,3138
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-36 kcal/mol
Surface area46140 Å2
Unit cell
Length a, b, c (Å)150.072, 84.366, 88.259
Angle α, β, γ (deg.)90, 113.403, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27460.793 Da / Num. of mol.: 4
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: DNA chain DNA (5'-D(P*CP*GP*GP*AP*CP*T*ORP*AP*CP*GP*GP*G)-3')


Mass: 3595.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3')


Mass: 3639.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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

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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M diammonium hydrogen citrate pH 4.9, 60% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6702 Å / Relative weight: 1
ReflectionResolution: 2.1→72.045 Å / Num. obs: 56982 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.994 / Net I/σ(I): 5.9
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2865 / CC1/2: 0.328

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→72.045 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.873 / SU B: 17.163 / SU ML: 0.211 / Cross valid method: FREE R-VALUE / ESU R: 0.486 / ESU R Free: 0.262
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 2374 5.045 %
Rwork0.2066 44683 -
all0.209 --
obs-47057 79.681 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.311 Å2
Baniso -1Baniso -2Baniso -3
1--0.331 Å20 Å20.166 Å2
2--0.021 Å20 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 2.1→72.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7732 970 0 242 8944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129103
X-RAY DIFFRACTIONr_bond_other_d00.0168215
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.84512572
X-RAY DIFFRACTIONr_angle_other_deg0.4261.71718947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16951002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.696568
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.748101297
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.57510370
X-RAY DIFFRACTIONr_chiral_restr0.0650.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210295
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022067
X-RAY DIFFRACTIONr_nbd_refined0.2090.21817
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.27633
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24222
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24387
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.277
X-RAY DIFFRACTIONr_nbd_other0.2260.2235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.227
X-RAY DIFFRACTIONr_mcbond_it1.4542.953993
X-RAY DIFFRACTIONr_mcbond_other1.4532.953993
X-RAY DIFFRACTIONr_mcangle_it2.5265.2985000
X-RAY DIFFRACTIONr_mcangle_other2.5265.2995001
X-RAY DIFFRACTIONr_scbond_it2.4513.9575110
X-RAY DIFFRACTIONr_scbond_other2.4513.9575110
X-RAY DIFFRACTIONr_scangle_it3.937.2077572
X-RAY DIFFRACTIONr_scangle_other3.937.2087573
X-RAY DIFFRACTIONr_lrange_it7.16143.57710304
X-RAY DIFFRACTIONr_lrange_other7.15743.60810278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.344230.3184280.3243290.9290.93710.41810.32
2.154-2.2130.333530.29110390.29342480.9270.94325.70620.29
2.213-2.2780.375790.28415750.28940960.8960.94540.38090.281
2.278-2.3480.3111160.28623000.28840070.9250.94160.29450.283
2.348-2.4250.2961580.27231210.27338730.9420.94984.6630.267
2.425-2.5090.3131770.26233710.26437580.9280.95394.41190.255
2.509-2.6040.2841850.25333820.25536420.9470.95897.94070.242
2.604-2.710.2751770.23132910.23334840.9450.96699.54080.217
2.71-2.8310.2561680.22731820.22933500.9610.9671000.212
2.831-2.9690.2831650.23330290.23631940.9430.9651000.215
2.969-3.1290.2841510.22729050.2330560.9470.9671000.21
3.129-3.3180.2391520.21127520.21229040.960.9731000.197
3.318-3.5470.2741310.225650.20326970.9560.97699.96290.191
3.547-3.830.2351250.18324020.18625340.9680.98199.72380.179
3.83-4.1950.221270.16922020.17223350.9740.98399.7430.173
4.195-4.6880.181080.14620060.14821230.980.98899.57610.156
4.688-5.4090.181910.15317630.15518610.9810.98899.62390.166
5.409-6.6150.226840.18115130.18415990.9750.98599.87490.194
6.615-9.3160.21650.14311770.14612470.9730.98999.5990.167
9.316-72.0450.302390.2066800.2117190.8490.9681000.254
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)
10.23870.067-0.10031.0523-0.04590.9993-0.00640.00070.03240.0339-0.0063-0.0517-0.00530.07790.01270.0126-0.015-0.00480.03360.00520.0089-31.2822-28.782915.3382
20.57620.02610.06541.2063-0.03910.60670.00490.0038-0.0063-0.049-0.02880.04410.01040.00430.02390.0097-0.0077-0.01170.0150.01120.0166-48.1631-29.3408-16.3975
30.20040.4472-0.0381.4684-0.07591.0991-0.0644-0.0142-0.0279-0.14160.0906-0.0003-0.0524-0.1712-0.02620.0240.0150.01070.06150.02330.013-62.6002-51.560826.7983
40.07570.1344-0.05910.9595-0.03791.8450.0218-0.0153-0.0269-0.08720.07240.1176-0.111-0.0216-0.09420.0313-0.0225-0.02530.02570.0260.06-61.576-5.354421.4087
Refinement TLS groupSelection: ALL

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