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- PDB-8jnk: Crystal structure of human ALKBH3 bound to ssDNA through active s... -

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Basic information

Entry
Database: PDB / ID: 8jnk
TitleCrystal structure of human ALKBH3 bound to ssDNA through active site crosslink
Components
  • (Synthetic antibody ...) x 2
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
  • DNA
KeywordsRNA BINDING PROTEIN / RNA m1A demethylase
Function / homology
Function and homology information


mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair ...mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / ferrous iron binding / cell population proliferation / DNA repair / mitochondrion / nucleoplasm / nucleus / cytosol
Similarity search - Function
Alkylated DNA repair protein alkB homologue 3 / 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
: / N-OXALYLGLYCINE / DNA / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsZhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation.
Authors: Zhang, L. / Duan, H.C. / Paduch, M. / Hu, J. / Zhang, C. / Mu, Y. / Lin, H. / He, C. / Kossiakoff, A.A. / Jia, G. / Zhang, L.
History
DepositionJun 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
B: DNA
C: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
D: DNA
E: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
F: DNA
G: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
H: DNA
I: Synthetic antibody heavy chain
J: Synthetic antibody heavy chain
K: Synthetic antibody heavy chain
L: Synthetic antibody heavy chain
M: Synthetic antibody light chain
N: Synthetic antibody light chain
O: Synthetic antibody light chain
P: Synthetic antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,61824
Polymers301,81016
Non-polymers8088
Water4,990277
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
B: DNA
G: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
H: DNA
I: Synthetic antibody heavy chain
K: Synthetic antibody heavy chain
M: Synthetic antibody light chain
O: Synthetic antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,30912
Polymers150,9058
Non-polymers4044
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
D: DNA
E: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
F: DNA
J: Synthetic antibody heavy chain
L: Synthetic antibody heavy chain
N: Synthetic antibody light chain
P: Synthetic antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,30912
Polymers150,9058
Non-polymers4044
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.460, 136.151, 203.390
Angle α, β, γ (deg.)90.00, 107.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 8 molecules IJKLMNOP

#3: Antibody
Synthetic antibody heavy chain /


Mass: 22927.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH3, ABH3 / Production host: Escherichia coli (E. coli)
#4: Antibody
Synthetic antibody light chain /


Mass: 23667.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH3, ABH3 / Production host: Escherichia coli (E. coli)

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Protein / DNA chain , 2 types, 8 molecules ACEGBDFH

#1: Protein
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 / Alkylated DNA repair protein alkB homolog 3 / hABH3


Mass: 27013.326 Da / Num. of mol.: 4 / Mutation: C110S, D189S, C201S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH3, ABH3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96Q83, DNA oxidative demethylase, mRNA N1-methyladenine demethylase
#2: DNA chain
DNA /


Mass: 1844.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 285 molecules

#5: Chemical
ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaCl, 20%PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 92893 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Χ2: 1.265 / Net I/σ(I): 11 / Num. measured all: 348882
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.69-2.793.50.68891521.269198.5
2.79-2.93.60.52392041.28198.6
2.9-3.033.70.35292551.279199
3.03-3.193.80.23292071.309199.4
3.19-3.393.80.14993221.374199.6
3.39-3.653.90.09692821.405199.6
3.65-4.023.90.06793281.34199.8
4.02-4.63.80.05193511.208199.8
4.6-5.793.80.04393911.067199.8
5.79-503.70.02894011.125198.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→46.9 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 4680 5.05 %
Rwork0.2176 --
obs0.2182 92717 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19635 456 11 277 20379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120651
X-RAY DIFFRACTIONf_angle_d1.25528193
X-RAY DIFFRACTIONf_dihedral_angle_d16.9417505
X-RAY DIFFRACTIONf_chiral_restr0.0743106
X-RAY DIFFRACTIONf_plane_restr0.023533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.720.35211830.34422793X-RAY DIFFRACTION97
2.72-2.750.36761810.3182886X-RAY DIFFRACTION98
2.75-2.780.3491730.3142873X-RAY DIFFRACTION98
2.79-2.820.32651470.30232911X-RAY DIFFRACTION98
2.82-2.860.29981370.28992893X-RAY DIFFRACTION98
2.86-2.90.27181390.28072937X-RAY DIFFRACTION99
2.9-2.940.34311450.27572948X-RAY DIFFRACTION98
2.94-2.980.30471170.2742897X-RAY DIFFRACTION99
2.98-3.030.2791330.26962992X-RAY DIFFRACTION99
3.03-3.080.27881430.26352872X-RAY DIFFRACTION99
3.08-3.130.29711650.26642975X-RAY DIFFRACTION99
3.13-3.190.29631470.26952890X-RAY DIFFRACTION99
3.19-3.250.28491450.26673008X-RAY DIFFRACTION99
3.25-3.320.25881600.24372902X-RAY DIFFRACTION100
3.32-3.390.25441590.24432932X-RAY DIFFRACTION99
3.39-3.470.26611580.23452928X-RAY DIFFRACTION100
3.47-3.550.26731230.23092982X-RAY DIFFRACTION99
3.55-3.650.23711350.2232954X-RAY DIFFRACTION100
3.65-3.760.21541570.22913027X-RAY DIFFRACTION100
3.76-3.880.21821480.21782905X-RAY DIFFRACTION100
3.88-4.020.21431950.21332899X-RAY DIFFRACTION100
4.02-4.180.20921790.20362934X-RAY DIFFRACTION100
4.18-4.370.20171430.18362989X-RAY DIFFRACTION100
4.37-4.60.18091500.1682945X-RAY DIFFRACTION100
4.6-4.880.19381440.16363008X-RAY DIFFRACTION100
4.88-5.260.17761780.18042941X-RAY DIFFRACTION100
5.26-5.790.19141840.19722941X-RAY DIFFRACTION100
5.79-6.620.21181730.19882976X-RAY DIFFRACTION100
6.63-8.340.21211540.19522980X-RAY DIFFRACTION100
8.34-46.90.1821850.17642919X-RAY DIFFRACTION96

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