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- PDB-6ie3: Crystal structure of methyladenine demethylase -

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Basic information

Entry
Database: PDB / ID: 6ie3
TitleCrystal structure of methyladenine demethylase
ComponentsNucleic acid dioxygenase ALKBH1
KeywordsOXIDOREDUCTASE / demethylase / DNA binding protein
Function / homology
Function and homology information


regulation of translational initiation by tRNA modification / positive regulation of gene expression, epigenetic / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA demethylase activity / oxidative RNA demethylation / tRNA wobble cytosine modification / DNA oxidative demethylase / regulation of mitochondrial translation ...regulation of translational initiation by tRNA modification / positive regulation of gene expression, epigenetic / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA demethylase activity / oxidative RNA demethylation / tRNA wobble cytosine modification / DNA oxidative demethylase / regulation of mitochondrial translation / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / 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 / RNA repair / 2-oxoglutarate-dependent dioxygenase activity / regulation of translational initiation / chemoattractant activity / developmental growth / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / placenta development / euchromatin / ferrous iron binding / neuron migration / neuron projection development / negative regulation of neuron apoptotic process / in utero embryonic development / tRNA binding / DNA repair / endoplasmic reticulum / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
ETHANOL / : / Nucleic acid dioxygenase ALKBH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsTian, L.F. / Tang, Q. / Chen, Z.Z. / Yan, X.X.
CitationJournal: Cell Res. / Year: 2020
Title: Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1.
Authors: Tian, L.F. / Liu, Y.P. / Chen, L. / Tang, Q. / Wu, W. / Sun, W. / Chen, Z. / Yan, X.X.
History
DepositionSep 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9893
Polymers43,8881
Non-polymers1012
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-2 kcal/mol
Surface area14560 Å2
Unit cell
Length a, b, c (Å)56.732, 56.732, 191.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nucleic acid dioxygenase ALKBH1 / Alkylated DNA repair protein alkB homolog 1 / Alpha-ketoglutarate-dependent dioxygenase ABH1 / DNA ...Alkylated DNA repair protein alkB homolog 1 / Alpha-ketoglutarate-dependent dioxygenase ABH1 / DNA 6mA demethylase / DNA N6-methyl adenine demethylase / DNA lyase ABH1 / DNA oxidative demethylase ALKBH1 / tRNA N1-methyl adenine demethylase


Mass: 43887.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH1, ABH, ABH1, ALKBH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13686, DNA N6-methyladenine demethylase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 5% ethanol, 5% MPD, 100 mM NaF, 100 mM HepespH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 24558 / % possible obs: 99.4 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.026 / Rrim(I) all: 0.099 / Net I/σ(I): 23.1
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.746 / Num. unique obs: 621 / Rpim(I) all: 0.232 / Rrim(I) all: 0.783

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.97→49.13 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.163 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 978 4.6 %RANDOM
Rwork0.20253 ---
obs0.20398 20188 86.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å2-0 Å2
2--0.15 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.97→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 4 283 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192502
X-RAY DIFFRACTIONr_bond_other_d0.0010.022233
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9523396
X-RAY DIFFRACTIONr_angle_other_deg0.87135167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97823.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71715384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.971515
X-RAY DIFFRACTIONr_chiral_restr0.0690.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5473.1851251
X-RAY DIFFRACTIONr_mcbond_other1.5453.1841250
X-RAY DIFFRACTIONr_mcangle_it2.7694.7521559
X-RAY DIFFRACTIONr_mcangle_other2.7684.7531560
X-RAY DIFFRACTIONr_scbond_it1.1693.2341251
X-RAY DIFFRACTIONr_scbond_other1.1683.2351252
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1234.8111837
X-RAY DIFFRACTIONr_long_range_B_refined5.33637.152791
X-RAY DIFFRACTIONr_long_range_B_other5.17436.7342750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 27 -
Rwork0.226 621 -
obs--35.72 %

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