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- PDB-7rds: Structure of human NTHL1 -

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Basic information

Entry
Database: PDB / ID: 7rds
TitleStructure of human NTHL1
ComponentsIsoform 3 of Endonuclease III-like protein 1
KeywordsHYDROLASE / Lyase / DNA Glycosylase
Function / homology
Function and homology information


Defective NTHL1 substrate processing / Defective NTHL1 substrate binding / : / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / DNA N-glycosylase activity / oxidized purine nucleobase lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds ...Defective NTHL1 substrate processing / Defective NTHL1 substrate binding / : / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / DNA N-glycosylase activity / oxidized purine nucleobase lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / endonuclease activity / damaged DNA binding / mitochondrion / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Endonuclease III-like protein 1 / Endonuclease III-like, conserved site-2 / Endonuclease III family signature. / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain ...Endonuclease III-like protein 1 / Endonuclease III-like, conserved site-2 / Endonuclease III family signature. / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Endonuclease III-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsCarroll, B.L. / Zahn, K.E. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA098993 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis.
Authors: Carroll, B.L. / Zahn, K.E. / Hanley, J.P. / Wallace, S.S. / Dragon, J.A. / Doublie, S.
History
DepositionJul 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 3 of Endonuclease III-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0172
Polymers28,6651
Non-polymers3521
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The enzyme elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.800, 124.800, 42.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Isoform 3 of Endonuclease III-like protein 1 / hNTH1 / Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase / DNA glycosylase/AP lyase


Mass: 28664.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTHL1, NTH1, OCTS3 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P78549, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 5K MME, Sodium chloride, Tricine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→40.85 Å / Num. obs: 13457 / % possible obs: 100 % / Redundancy: 22.2 % / Biso Wilson estimate: 50.72 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.077 / Net I/σ(I): 5.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 22.3 % / Num. unique obs: 1567 / CC1/2: 0.181 / Rpim(I) all: 0.619 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→40.85 Å / SU ML: 0.3369 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 31.3585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 1285 5.05 %
Rwork0.1996 24138 -
obs0.202 25423 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 8 115 1925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021856
X-RAY DIFFRACTIONf_angle_d0.43092533
X-RAY DIFFRACTIONf_chiral_restr0.0343286
X-RAY DIFFRACTIONf_plane_restr0.0069322
X-RAY DIFFRACTIONf_dihedral_angle_d11.3133685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.31891340.33242652X-RAY DIFFRACTION99.96
2.6-2.720.34261170.30632701X-RAY DIFFRACTION99.89
2.72-2.860.28951320.26452732X-RAY DIFFRACTION99.97
2.86-3.040.284920.28932703X-RAY DIFFRACTION100
3.04-3.280.31341980.26412672X-RAY DIFFRACTION100
3.28-3.60.24551620.20072627X-RAY DIFFRACTION100
3.61-4.130.2111540.18242689X-RAY DIFFRACTION100
4.13-5.20.2161250.15152704X-RAY DIFFRACTION100
5.2-40.850.21981710.15172658X-RAY DIFFRACTION99.72
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)
16.07917210101-3.49837965019-1.298321037137.396944353072.676264598811.56535032349-0.5526908987940.183653968923-1.03147776302-0.621434851667-0.2639387214931.55623627252-0.560610684886-0.3053417312650.3595469358930.760481278102-0.322829685294-0.04950052520941.487452895270.383947802710.929304926971-54.57551.26416.678
23.033052134410.355975594503-1.271728805015.338664640480.6208386431215.21222350783-0.274266795584-0.0361921791457-0.213666130482-0.1513853997220.05624933299740.1838154966440.684707017976-0.2726463880560.1632686314570.419718398193-0.2549219944780.03599336147790.560408118470.02333745929440.283430745515-35.59247.3121.617
37.86201711011-1.61761991676-1.788373331710.6094357538391.213008131162.850174678020.524371684668-1.143405088090.2767850836720.0436842301943-0.275425168088-0.205324696717-0.38808292055-0.535302201968-0.2813757141840.529849535625-0.110896204173-0.05043325292171.112003043970.07257178827170.646938787397-61.91761.86617.999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 89:124 )A89 - 124
2X-RAY DIFFRACTION2( CHAIN A AND RESID 125:229 )A125 - 229
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 230:317 OR RESID 401:401 ) )A230 - 317
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 230:317 OR RESID 401:401 ) )A401

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