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- PDB-6ie2: Crystal structure of methyladenine demethylase -

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Basic information

Entry
Database: PDB / ID: 6ie2
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 / DNA oxidative demethylase / tRNA wobble cytosine modification / 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 / DNA oxidative demethylase / tRNA wobble cytosine modification / regulation of mitochondrial translation / broad specificity oxidative DNA demethylase activity / oxidative RNA 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 / ferrous iron binding / euchromatin / neuron migration / neuron projection development / in utero embryonic development / negative regulation of neuron apoptotic process / 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
2-OXOGLUTARIC ACID / : / Nucleic acid dioxygenase ALKBH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Nov 22, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleic acid dioxygenase ALKBH1
B: Nucleic acid dioxygenase ALKBH1
C: Nucleic acid dioxygenase ALKBH1
D: Nucleic acid dioxygenase ALKBH1
E: Nucleic acid dioxygenase ALKBH1
F: Nucleic acid dioxygenase ALKBH1
G: Nucleic acid dioxygenase ALKBH1
H: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,71024
Polymers351,1018
Non-polymers1,60816
Water8,755486
1
A: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Nucleic acid dioxygenase ALKBH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0893
Polymers43,8881
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.017, 99.170, 126.793
Angle α, β, γ (deg.)106.60, 90.42, 93.14
Int Tables number1
Space group name H-MP1

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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.: 8
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.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5% PEG3350, 5% MPD, 100mM CaCl2, 200mM NaF, 100mM Bis-Tris pH6.5
PH range: 6.2-7.0

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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: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.8→50.01 Å / Num. obs: 72797 / % possible obs: 93 % / Redundancy: 3.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 1351 / CC1/2: 0.643 / Rpim(I) all: 0.556

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IE3

6ie3


Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.611 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25357 3700 5.1 %RANDOM
Rwork0.21644 ---
obs0.21835 69068 71.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.06 Å2-0.88 Å2
2--1.53 Å2-0.5 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20086 0 88 486 20660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01920739
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218392
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.95228155
X-RAY DIFFRACTIONr_angle_other_deg0.919342551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59652555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74523.28930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.811153179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.51815125
X-RAY DIFFRACTIONr_chiral_restr0.070.22975
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02123310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024507
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_it2.2175.49410295
X-RAY DIFFRACTIONr_mcbond_other2.2165.49410294
X-RAY DIFFRACTIONr_mcangle_it3.8898.22112825
X-RAY DIFFRACTIONr_mcangle_other3.8898.22212826
X-RAY DIFFRACTIONr_scbond_it1.755.49710444
X-RAY DIFFRACTIONr_scbond_other1.755.49710440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1728.20515327
X-RAY DIFFRACTIONr_long_range_B_refined6.82361.26822044
X-RAY DIFFRACTIONr_long_range_B_other6.81661.27222030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 65 -
Rwork0.291 1351 -
obs--18.73 %

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