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- PDB-4hp3: Crystal structure of Tet3 in complex with a CpG dsDNA -

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Basic information

Entry
Database: PDB / ID: 4hp3
TitleCrystal structure of Tet3 in complex with a CpG dsDNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
  • LOC100036628 protein
KeywordsDNA BINDING PROTEIN/DNA / CXXC / DNA methylation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


methylcytosine dioxygenase / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / methyl-CpG binding / DNA demethylation / chromosome / chromatin organization / regulation of gene expression / 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 tet3
Similarity search - Component
Biological speciesXENOPUS TROPICALIS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsChao, X. / Tempel, W. / Bian, C. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development.
Authors: Xu, Y. / Xu, C. / Kato, A. / Tempel, W. / Abreu, J.G. / Bian, C. / Hu, Y. / Hu, D. / Zhao, B. / Cerovina, T. / Diao, J. / Wu, F. / He, H.H. / Cui, Q. / Clark, E. / Ma, C. / Barbara, A. / ...Authors: Xu, Y. / Xu, C. / Kato, A. / Tempel, W. / Abreu, J.G. / Bian, C. / Hu, Y. / Hu, D. / Zhao, B. / Cerovina, T. / Diao, J. / Wu, F. / He, H.H. / Cui, Q. / Clark, E. / Ma, C. / Barbara, A. / Veenstra, G.J. / Xu, G. / Kaiser, U.B. / Liu, X.S. / Sugrue, S.P. / He, X. / Min, J. / Kato, Y. / Shi, Y.G.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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*AP*CP*GP*TP*TP*GP*GP*C)-3')
B: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
C: LOC100036628 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8888
Polymers15,7573
Non-polymers1315
Water41423
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-18 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.892, 39.455, 54.134
Angle α, β, γ (deg.)90.000, 99.920, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein LOC100036628 protein


Mass: 8430.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog)
Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: A0JP82
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / 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.: 23 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.05→34.42 Å / Num. obs: 9281 / % possible obs: 99.79 % / Redundancy: 3.71 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.5727
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.05-2.163.710.6749961345199.85
2.16-2.293.720.3947111267199.92
2.29-2.453.750.2445231206199.79
2.45-2.653.750.1441691111199.81
2.65-2.93.730.138401029199.75
2.9-3.243.730.063456926199.89
3.24-3.743.730.043078825199.68
3.74-4.583.70.042619708199.7
4.58-6.483.590.041976550199.9
6.48-34.423.350.041052314199.03

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model of complex between same protein construct and a methylated DNA fragment. That structure was solved by a combination of zinc-SAD (SHELXD/E) and molecular replacement ...Starting model: unpublished model of complex between same protein construct and a methylated DNA fragment. That structure was solved by a combination of zinc-SAD (SHELXD/E) and molecular replacement in "density" mode (MOLREP), using ideal DNA (COOT) and human MLL2 (currently unpublished) as search models.

Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.214 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. COOT and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 452 4.87 %RANDOM
Rwork0.2155 ---
obs0.217 9281 99.678 %-
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 max: 122.83 Å2 / Biso mean: 52.769 Å2 / Biso min: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20.395 Å2
2---0.739 Å20 Å2
3---1.875 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms384 486 5 23 898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.014940
X-RAY DIFFRACTIONr_bond_other_d0.0030.02662
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.6021359
X-RAY DIFFRACTIONr_angle_other_deg1.163.011530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.013550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3422014
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.941579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.48156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.1030.415320.32165168599.708
2.103-2.160.345300.278631661100
2.16-2.2230.288350.268628663100
2.223-2.2910.297270.26756859699.832
2.291-2.3650.187240.24360162699.84
2.365-2.4480.292320.23254257699.653
2.448-2.540.312250.23853155899.642
2.54-2.6420.365280.257527555100
2.642-2.7590.264190.28849051299.414
2.759-2.8920.278220.287499521100
2.892-3.0470.312330.24436469100
3.047-3.230.289280.2542445399.779
3.23-3.450.244250.17839942699.531
3.45-3.7230.178140.238239799.748
3.723-4.0720.201240.18935337999.472
4.072-4.5420.135170.16631733599.701
4.542-5.2240.225140.19128229799.663
5.224-6.3510.22380.183249257100
6.351-8.7860.19270.18819620599.024
8.786-300.26680.19312013098.462
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)
14.09495.251-0.6899.47110.45654.6317-0.64840.9541-0.2178-0.55340.51980.1219-0.08170.03590.12860.2734-0.21140.08670.5299-0.10940.1427-18.4712-18.9198.1644
29.51266.45320.55327.80030.91415.0148-0.16530.30010.0626-0.40540.13930.29390.1253-0.26410.0260.2464-0.0713-0.01690.34590.01360.1683-18.7733-18.05529.3508
33.86360.4324-2.173110.30050.30645.4021-0.07720.37380.003-0.54850.1085-0.0284-0.1633-0.1043-0.03130.275-0.06990.02210.1512-0.00650.0413-19.7853-17.356719.5889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C59 - 109

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