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- PDB-6ksf: Crystal Structure of ALKBH1 bound to 21-mer DNA bulge -

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Basic information

Entry
Database: PDB / ID: 6ksf
TitleCrystal Structure of ALKBH1 bound to 21-mer DNA bulge
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1
  • DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')
  • DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')
KeywordsGENE REGULATION / DNA methylation / complex / demethylase
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 wobble cytosine modification / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase ...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 wobble cytosine modification / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / 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 / DNA alkylation 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 / neuron migration / ferrous iron binding / placenta development / euchromatin / neuron projection development / regulation of gene expression / in utero embryonic development / negative regulation of neuron apoptotic process / tRNA binding / cell differentiation / 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
SUCCINIC ACID / propane-1-thiol / DNA / DNA (> 10) / Nucleic acid dioxygenase ALKBH1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, H. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31725014 China
CitationJournal: Cell Res. / Year: 2020
Title: Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA.
Authors: Zhang, M. / Yang, S. / Nelakanti, R. / Zhao, W. / Liu, G. / Li, Z. / Liu, X. / Wu, T. / Xiao, A. / Li, H.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 22, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1
B: DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')
C: DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1097
Polymers51,8443
Non-polymers2654
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.482, 67.482, 263.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 1


Mass: 38087.344 Da / Num. of mol.: 1 / Fragment: BRD4-Bromo2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ALKBH1 / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CB42*PLUS

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DCP*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3')


Mass: 7378.727 Da / Num. of mol.: 1 / Fragment: histone H2A.Z peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DTP*DCP*DAP*DGP*DC)-3')


Mass: 6378.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 67 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M NaCl, 0.1 M phosphate citrate, pH 4.2,10% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2019 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24642 / % possible obs: 98.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Χ2: 0.779 / Net I/σ(I): 7.1 / Num. measured all: 202846
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.448.60.71611830.8960.2360.7560.43397.8
2.44-2.498.40.63811920.8750.2110.6740.4698.3
2.49-2.538.40.611880.9040.20.6350.43898.3
2.53-2.598.20.52612010.9090.1770.5570.4598.5
2.59-2.648.20.42112020.9420.1430.4470.46698.4
2.64-2.77.70.32612040.9590.1140.3460.47998.9
2.7-2.778.40.31411890.9690.1060.3320.48798.8
2.77-2.858.60.25511990.9740.0840.270.49697.6
2.85-2.938.40.20612310.980.0690.2180.5199.4
2.93-3.028.50.15711990.9880.0530.1660.57899.3
3.02-3.138.30.1312230.9910.0440.1380.61799.3
3.13-3.267.90.09312340.9960.0320.0990.77699.4
3.26-3.418.20.07612290.9970.0250.080.9498.8
3.41-3.588.50.07412320.9960.0250.0780.99899.5
3.58-3.818.50.06712350.9970.0230.0721.00599.3
3.81-4.180.06112460.9970.0220.0661.18999.3
4.1-4.528.30.05712770.9980.020.061.28999.4
4.52-5.178.30.05212730.9980.0180.0551.28999.3
5.17-6.5180.05212950.9980.0190.0561.19298.8
6.51-507.30.04714100.9980.0180.0511.497.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IMC

6imc


Resolution: 2.4→32.888 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 1203 4.9 %0
Rwork0.2281 ---
obs0.2302 24541 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.33 Å2 / Biso mean: 57.3443 Å2 / Biso min: 24.68 Å2
Refinement stepCycle: final / Resolution: 2.4→32.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 912 14 63 3661
Biso mean--51.28 48.28 -
Num. residues----380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.4980.30841350.2885250598
2.498-2.61170.36791510.2882249698
2.6117-2.74930.30741340.2739252099
2.7493-2.92140.33651280.2949255699
2.9214-3.14680.31481280.2687256799
3.1468-3.46320.25991260.2373259499
3.4632-3.96360.26741380.2281263499
3.9636-4.99090.241090.1943267299
4.9909-32.8880.24431540.199279498

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