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- PDB-5deu: Crystal structure of TET2-5hmC complex -

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Basic information

Entry
Database: PDB / ID: 5deu
TitleCrystal structure of TET2-5hmC complex
Components
  • DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')
  • Methylcytosine dioxygenase TET2, chimeric construct
Keywordsoxidoreductase/DNA / 5-methylcytosine dioxygenase / TET2 / 5hmC / protein-DNA complex / oxidoreductase-DNA complex
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
: / N-OXALYLGLYCINE / DNA / DNA (> 10) / Methylcytosine dioxygenase TET2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsHu, L. / Cheng, J. / Rao, Q. / Li, Z. / Li, J. / Xu, Y.
CitationJournal: Nature / Year: 2015
Title: Structural insight into substrate preference for TET-mediated oxidation.
Authors: Hu, L. / Lu, J. / Cheng, J. / Rao, Q. / Li, Z. / Hou, H. / Lou, Z. / Zhang, L. / Li, W. / Gong, W. / Liu, M. / Sun, C. / Yin, X. / Li, J. / Tan, X. / Wang, P. / Wang, Y. / Fang, D. / Cui, Q. ...Authors: Hu, L. / Lu, J. / Cheng, J. / Rao, Q. / Li, Z. / Hou, H. / Lou, Z. / Zhang, L. / Li, W. / Gong, W. / Liu, M. / Sun, C. / Yin, X. / Li, J. / Tan, X. / Wang, P. / Wang, Y. / Fang, D. / Cui, Q. / Yang, P. / He, C. / Jiang, H. / Luo, C. / Xu, Y.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcytosine dioxygenase TET2, chimeric construct
B: DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')
C: DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,10110
Polymers58,4713
Non-polymers6307
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-36 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.262, 87.522, 260.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methylcytosine dioxygenase TET2, chimeric construct


Mass: 51397.352 Da / Num. of mol.: 1 / Fragment: unp residues 1129-1480, 1844-1935
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TET2, KIAA1546, Nbla00191 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6N021, 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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')


Mass: 3693.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3')


Mass: 3380.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 6 types, 316 molecules

#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-FE / FE (III) ION


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


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 26% PEGMME2000,0.1M MES6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50752 / % possible obs: 98 % / Redundancy: 9.6 % / Biso Wilson estimate: 31.67 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.054 / Net I/av σ(I): 19.219 / Net I/σ(I): 16.3 / Num. measured all: 487032
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.864.80.82845231.09188.6
1.86-1.9460.53849191.09996.4
1.94-2.037.70.36750891.08699.7
2.03-2.13110.24551101.095100
2.13-2.2711.30.18351631.069100
2.27-2.4411.30.13451111.047100
2.44-2.6911.30.10651721.017100
2.69-3.0811.20.08551931.00999.9
3.08-3.8810.80.08652411.04199.7
3.88-509.70.07952311.04595.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM6

4nm6


Resolution: 1.801→42.262 Å / FOM work R set: 0.838 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1995 3.94 %
Rwork0.1771 48691 -
obs0.1785 50686 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.93 Å2 / Biso mean: 45.98 Å2 / Biso min: 19.87 Å2
Refinement stepCycle: final / Resolution: 1.801→42.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 472 27 309 4060
Biso mean--44.75 46.64 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063873
X-RAY DIFFRACTIONf_angle_d1.155320
X-RAY DIFFRACTIONf_chiral_restr0.072575
X-RAY DIFFRACTIONf_plane_restr0.004612
X-RAY DIFFRACTIONf_dihedral_angle_d18.9471504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8011-1.84610.29421330.27633038317187
1.8461-1.8960.29611180.24593256337494
1.896-1.95180.25691460.21773431357798
1.9518-2.01480.26181460.207835383684100
2.0148-2.08680.22221430.191635083651100
2.0868-2.17040.23531430.182135143657100
2.1704-2.26920.22331410.184735143655100
2.2692-2.38880.23291450.183435233668100
2.3888-2.53840.26051440.190835183662100
2.5384-2.73440.2451480.196535533701100
2.7344-3.00950.24361440.191835703714100
3.0095-3.44480.23211460.173835673713100
3.4448-4.33940.16761490.14743576372599
4.3394-42.27410.17411490.16533585373495
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)
13.08610.9006-1.24364.61160.2853.65860.10040.28870.626-0.2838-0.08260.1858-0.8958-0.1626-0.00520.5153-0.037-0.11380.29160.05240.31720.519914.8399-50.0884
22.80480.33860.34052.1748-0.16522.41580.00370.23660.011-0.2882-0.05070.0728-0.22890.0980.04450.27070.023-0.10060.2124-0.02960.239917.76861.5511-49.6589
32.45710.2391-0.89173.0080.34514.0494-0.0758-0.2931-0.25080.420.03210.41580.1756-0.34780.06540.2667-0.0447-0.06810.24780.03010.383210.74-9.4191-26.8105
41.9928-0.35010.45642.21840.0382.6666-0.099-0.2713-0.07570.40490.0244-0.2441-0.3210.19630.03550.3306-0.0376-0.17270.24280.03380.329522.43083.4451-24.0232
52.4863-1.09470.76591.1368-1.56293.21070.04670.0941-0.2598-0.2689-0.05020.0860.07970.080.00690.21180.0093-0.09740.1937-0.0070.354616.1264-5.7309-40.4048
64.83780.0819-3.1971.6325-0.46575.1712-0.31970.2545-0.3507-0.21240.05130.46170.3215-0.55010.25750.33210.011-0.17180.3037-0.06970.46633.1796-5.8466-48.461
71.4904-0.23970.74631.6496-0.15972.7976-0.0677-0.1878-0.00560.138-0.02930.0114-0.3783-0.04490.11380.2247-0.0028-0.10470.19490.01830.326716.37141.9453-29.661
86.2875-0.9077-1.57074.1390.6090.36860.2189-0.3422-0.10210.3839-0.34180.8913-0.36750.05910.06320.5393-0.0375-0.11410.29320.02140.39085.17358.9239-15.5698
93.9142-0.39891.9282.8152-3.21429.14110.26410.0378-0.1781-0.26030.10370.72160.2431-0.2611-0.28030.63570.1315-0.14190.3196-0.04340.47033.752413.1415-18.5934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1132 through 1168 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1169 through 1237 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1238 through 1282 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1283 through 1385 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1386 through 1423 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1424 through 1861 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1862 through 1921 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 12 )C0

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