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- PDB-9hxv: Crystal structure of TET2-DNA in complex with IOX1 -

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Basic information

Entry
Database: PDB / ID: 9hxv
TitleCrystal structure of TET2-DNA in complex with IOX1
Components
  • 12mer-DNA
  • Methylcytosine dioxygenase TET2
KeywordsOXIDOREDUCTASE / IOX1 / TET2
Function / homology
Function and homology information


leukocyte differentiation / methylcytosine dioxygenase / DNA 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / Specification of primordial germ cells / positive regulation of gene expression via chromosomal CpG island demethylation / myeloid cell differentiation / protein O-linked glycosylation / ferrous iron binding ...leukocyte differentiation / methylcytosine dioxygenase / DNA 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / Specification of primordial germ cells / positive regulation of gene expression via chromosomal CpG island demethylation / myeloid cell differentiation / protein O-linked glycosylation / ferrous iron binding / : / chromosome / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methylcytosine dioxygenase TET1/2/3 / : / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily
Similarity search - Domain/homology
8-hydroxyquinoline-5-carboxylic acid / : / DNA / DNA (> 10) / Methylcytosine dioxygenase TET2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNiggenaber, J. / Mueller, M.P. / Rauh, D.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research01ZX2201B Germany
European Regional Development FundEFRE-800400European Union
Other governmentNW21-062C
Other privateEx-2021-0033
German Research Foundation (DFG) Germany
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Advancing TET Inhibitor Development: From Structural Insights to Biological Evaluation.
Authors: Willems, S. / Maksumic, L. / Niggenaber, J. / Lin, T.C. / Schulz, T. / Weisner, J. / Sievers, S. / Muller, M.P. / Summerer, D. / Rauh, D.
History
DepositionJan 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcytosine dioxygenase TET2
B: 12mer-DNA
C: 12mer-DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,79310
Polymers59,2213
Non-polymers5737
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-39 kcal/mol
Surface area20460 Å2
Unit cell
Length a, b, c (Å)48.440, 89.130, 268.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein Methylcytosine dioxygenase TET2


Mass: 51867.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TET2, KIAA1546, Nbla00191 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6N021, methylcytosine dioxygenase
#2: DNA chain 12mer-DNA


Mass: 3676.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 242 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-8XQ / 8-hydroxyquinoline-5-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24 % PEG 2000MME, 100 mM MES pH 7.0 25 mg/mL protein 1:1 with DNA plus 5 mM IOX1 Seeding experiment (1 ul reservoir + 1 ul protein:DNA:IOX1 + 0.2 ul seeding solution)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 25, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 45640 / % possible obs: 98.3 % / Redundancy: 13.43 % / Biso Wilson estimate: 31.82 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.106 / Net I/σ(I): 17.08
Reflection shellResolution: 1.9→2 Å / Redundancy: 12.43 % / Mean I/σ(I) obs: 2.74 / Num. unique obs: 6070 / CC1/2: 0.526 / Rrim(I) all: 1.141 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.56 Å / SU ML: 0.2495 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 2281 5 %
Rwork0.1896 43354 -
obs0.1912 45635 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 494 24 235 3862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333777
X-RAY DIFFRACTIONf_angle_d0.63225222
X-RAY DIFFRACTIONf_chiral_restr0.0435571
X-RAY DIFFRACTIONf_plane_restr0.0043601
X-RAY DIFFRACTIONf_dihedral_angle_d17.46011444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.37281240.31462364X-RAY DIFFRACTION85.79
1.94-1.990.31331390.27972644X-RAY DIFFRACTION98.97
1.99-2.040.31271420.26112701X-RAY DIFFRACTION98.27
2.04-2.090.27171420.23392702X-RAY DIFFRACTION99.86
2.09-2.150.30321410.23452663X-RAY DIFFRACTION99.01
2.15-2.220.25751430.22352726X-RAY DIFFRACTION98.9
2.22-2.30.26181450.22232742X-RAY DIFFRACTION99.59
2.3-2.390.24541420.21062702X-RAY DIFFRACTION99.72
2.39-2.50.25421420.21142708X-RAY DIFFRACTION99.27
2.5-2.630.25341440.2062724X-RAY DIFFRACTION99.48
2.63-2.80.2191430.20262717X-RAY DIFFRACTION98.32
2.8-3.020.21221440.19972752X-RAY DIFFRACTION99.79
3.02-3.320.22151450.19162749X-RAY DIFFRACTION99.66
3.32-3.80.18191470.16962781X-RAY DIFFRACTION99.76
3.8-4.780.17881480.14822812X-RAY DIFFRACTION99.73
4.79-42.560.21500.16512867X-RAY DIFFRACTION96.98
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)
13.75793281479-2.58161589957-1.567659882761.998713491411.071642156330.7749114765520.2573210192330.4825236851830.271955321073-0.647551678765-0.2121016369020.361864291612-0.789695111861-0.4801541757660.04975382016410.4916067171360.0194633746633-0.07995102588030.3019705975730.06177173382040.40309422054317.280423405517.8621972341-50.486961352
21.716018949030.571228168069-0.1356275981261.92296079371-0.2442891387662.025225479410.02625662614660.1967365118960.0623998697266-0.190129012649-0.0293797535558-0.211151515262-0.1654489404930.1244334723260.005845794491820.2546152843050.0107386520557-0.02690562765520.266304995225-0.01146302076490.21840559331620.02278162623.0362327131-51.6341741471
33.232792713590.578794039297-0.3227641655121.111168374280.3242729750991.864265206380.0230235727747-0.372603835412-0.2754357668130.291764011729-0.0323728340545-0.008803996221040.129573256077-0.1227903262520.006983983490110.322143244076-0.0267307859191-0.08141957801490.2897308763420.05816915943920.32150448122310.811192006-8.73125321485-28.5290840805
41.87255088699-0.2946057948660.09009961596131.77956475307-0.1344854135651.30075594051-0.0184961846681-0.324114196740.02284412013760.4643116272340.00334682831149-0.40847967617-0.2034136285950.1437211457420.03136949042460.335157587274-0.0323033739225-0.1514189192240.2709159704460.006781301753480.30134481333822.72051903324.34612337683-26.0532504281
51.83848709239-0.219242161480.06003113903121.14028500352-0.828528718271.78969157970.005143113480010.166835063632-0.2049898254-0.18166235103-0.118832808161-0.2592919049420.09920786106110.002061848311090.06394005214180.2520416489710.00902896174804-0.05282080837060.239823424607-0.008384173305660.3136904453816.4498995383-4.43963576732-41.7568709355
63.083774721970.791894398415-2.250395360131.15337757935-0.872188734293.10938469185-0.2006378991080.492180705303-0.242658029854-0.2139941650930.1297275441510.2165058665510.242667620409-0.4794623995920.05615815544410.3530801051470.00280691214051-0.08635528611460.319268950272-0.04663997425770.3464077279383.53817078791-5.2998872622-50.8682042849
71.22455475126-0.1185243732710.3319500620521.08615124437-0.2378273769741.1214051765-0.00574411237993-0.129266884617-0.04651606795220.1894111898320.0290276358007-0.12986533551-0.149174017799-0.000824969143606-0.02194974900650.2828666220120.000434719143813-0.09378272558430.241365479961-0.002407284036540.30681949978316.77950857641.82859242958-32.3226297109
81.899010638211.40470911305-0.8494041343953.928723519280.4096334254211.36073381637-0.0308692982209-0.4926384908920.1808544731560.126766024714-0.3828016420542.2927074197-1.31961891045-1.05266428848-0.128974220440.7374125635310.278032002609-0.4984729625590.6530446744060.102024625060.1942785392394.9401196986510.7176999654-19.3240191155
90.0930471294316-0.197925748743-0.0168883756690.5062817955950.08979199356030.0522315793197-0.0465473872332-0.08120124518130.056524489754-0.0206084616682-0.05303913915510.0706339818890.0164646070631-0.01770190678310.0006319248001251.761517730270.1133611157780.2685275147671.706046476370.3327751290490.8208475699482.606049409577.708239513841.00606771783
101.877560899640.4092703147120.09693241893342.85450259484-1.231345499114.678904261850.0469429839581-0.516202717264-0.308398111595-0.480013663987-0.3135917220531.51329925025-0.140417557851-0.6456564939890.1834408042521.035197543340.215290542436-0.1888058384650.9590370075630.08125459279640.5680651596453.8832408659812.5439650576-18.6543799747
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1132 through 1156 )AA1132 - 11561 - 20
22chain 'A' and (resid 1157 through 1237 )AA1157 - 123721 - 101
33chain 'A' and (resid 1238 through 1282 )AA1238 - 1282102 - 146
44chain 'A' and (resid 1283 through 1385 )AA1283 - 1385147 - 249
55chain 'A' and (resid 1386 through 1423 )AA1386 - 1423250 - 287
66chain 'A' and (resid 1424 through 1861 )AA1424 - 1861288 - 347
77chain 'A' and (resid 1862 through 1919 )AA1862 - 1919348 - 405
88chain 'B' and (resid 1 through 11 )BG1 - 11
99chain 'B' and (resid 12 through 12 )BG12
1010chain 'C' and (resid 1 through 12 )CH1 - 12

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