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- PDB-6asd: Zinc finger region of human TET1 in complex with CpG DNA -

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Basic information

Entry
Database: PDB / ID: 6asd
TitleZinc finger region of human TET1 in complex with CpG DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')
  • Methylcytosine dioxygenase TET1
KeywordsDNA BINDING PROTEIN/DNA / zinc finger / dna-binding / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


: / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / inner cell mass cell differentiation / : / negative regulation of DNA methylation-dependent heterochromatin formation / protein O-linked glycosylation / oxidative demethylation / methyl-CpG binding ...: / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / inner cell mass cell differentiation / : / negative regulation of DNA methylation-dependent heterochromatin formation / protein O-linked glycosylation / oxidative demethylation / methyl-CpG binding / DNA demethylation / stem cell population maintenance / chromatin organization / iron ion binding / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Methylcytosine dioxygenase TET1/2/3 / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Methylcytosine dioxygenase TET1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, K. / Xu, C. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionAug 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')
B: DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')
C: Methylcytosine dioxygenase TET1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,96422
Polymers12,8333
Non-polymers13119
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-14 kcal/mol
Surface area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.502, 31.951, 65.414
Angle α, β, γ (deg.)90.000, 121.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')


Mass: 3664.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Protein/peptide Methylcytosine dioxygenase TET1 / CXXC-type zinc finger protein 6 / Leukemia-associated protein with a CXXC domain / Ten-eleven ...CXXC-type zinc finger protein 6 / Leukemia-associated protein with a CXXC domain / Ten-eleven translocation 1 gene protein


Mass: 5504.574 Da / Num. of mol.: 1 / Fragment: Zinc finger region (UNP residues 587-632)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TET1, CXXC6, KIAA1676, LCX / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q8NFU7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 25% PEG-3350, 0.2 M ammonium acetate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→36.72 Å / Num. obs: 11082 / % possible obs: 98.3 % / Redundancy: 3.6 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.023 / Rrim(I) all: 0.044 / Net I/σ(I): 22.1 / Num. measured all: 40255 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.893.80.42325756760.8720.2520.4943.295.7
9.06-36.7230.0293041020.9980.0190.03553.891.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4hp3

4hp3


Resolution: 1.85→36.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.58 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.131
Details: coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflection
Rfree0.235 539 4.9 %
Rwork0.2016 --
obs0.2033 10543 98.13 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.8 Å2 / Biso mean: 36.226 Å2 / Biso min: 22.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20.3 Å2
2--0.37 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.85→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms348 486 19 58 911
Biso mean--35.78 39.37 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.014913
X-RAY DIFFRACTIONr_bond_other_d0.0040.02619
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.461322
X-RAY DIFFRACTIONr_angle_other_deg1.3363.0111447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.799548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.54823.33315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4921584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.978154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02685
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02199
X-RAY DIFFRACTIONr_mcbond_it1.1882.21182
X-RAY DIFFRACTIONr_mcbond_other1.1872.207181
X-RAY DIFFRACTIONr_mcangle_it1.743.305227
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 44 -
Rwork0.241 765 -
all-809 -
obs--96.2 %
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)
17.7973-2.0198-0.7141.8113-0.54340.6956-0.144-0.1623-0.189-0.0040.2018-0.02080.0541-0.0592-0.05780.06530.058-0.00120.1101-0.00710.0898-65.544228.723411.3996
27.5508-3.0152-1.3143.41030.07491.2032-0.050.2297-0.2054-0.08350.01460.0660.0214-0.01340.03540.0510.05-0.01040.11340.0080.0436-65.108829.63239.9697
33.83972.4037-0.97876.8408-1.41684.810.0258-0.17840.06320.63480.1264-0.1477-0.2363-0.0045-0.15220.1420.0975-0.01050.0947-0.00470.0142-64.846839.164518.8573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C586 - 630

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