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- PDB-8jnr: Crystal structure of human ALKBH3 bound to 3mC containing ssDNA t... -

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Basic information

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


mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / negative regulation of cytoplasmic translation / ferrous iron binding ...mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / negative regulation of cytoplasmic translation / ferrous iron binding / cell population proliferation / DNA repair / mitochondrion / nucleoplasm / 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
Chem-ME6 / : / N-OXALYLGLYCINE / DNA / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.66 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 / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 30, 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

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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: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
E: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3
F: DNA
G: Synthetic antibody heavy chain
H: Synthetic antibody heavy chain
I: Synthetic antibody heavy chain
J: Synthetic antibody heavy chain
K: Synthetic antibody light chain
L: Synthetic antibody light chain
M: Synthetic antibody light chain
N: Synthetic antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,72321
Polymers298,88714
Non-polymers8367
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34110 Å2
ΔGint-182 kcal/mol
Surface area106530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.615, 142.171, 130.110
Angle α, β, γ (deg.)90.00, 113.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules GHIJKLMN

#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) / 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) / Production host: Escherichia coli (E. coli)

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Protein / DNA chain , 2 types, 6 molecules ACDEBF

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


Mass: 27693.117 Da / Num. of mol.: 4 / Mutation: D110S, D189C, 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: 867.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 7 molecules

#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-ME6 / [(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate


Type: DNA linking / Mass: 322.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O7P / Feature type: SUBJECT OF INVESTIGATION

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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: 3.1 Å3/Da / Density % sol: 60.26 %
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 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 3.66→50 Å / Num. obs: 35958 / % possible obs: 89.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.244 / Χ2: 1.499 / Net I/σ(I): 5.2 / Num. measured all: 97662
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.66-3.722.70.69418241.805192
3.72-3.792.70.97518151.544191.9
3.79-3.862.70.9618421.487192.4
3.86-3.942.70.96418321.442191.6
3.94-4.032.71.817981.417191.1
4.03-4.122.70.78118201.451191.7
4.12-4.222.70.68718251.467190.9
4.22-4.342.70.43318141.508190.6
4.34-4.472.70.32618071.635190.7
4.47-4.612.70.30518001.475190.7
4.61-4.782.70.26817791.547190.4
4.78-4.972.70.23718301.552190.2
4.97-5.192.70.25317811.534189.7
5.19-5.472.70.23418001.555190.2
5.47-5.812.70.24117741.588189
5.81-6.262.70.20417861.5188.6
6.26-6.882.70.17317521.44188
6.88-7.882.70.11717811.402188.1
7.88-9.912.80.06517691.409187.4
9.91-502.80.04417291.238183.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UIW

2uiw


Resolution: 3.66→34.38 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1986 5.59 %
Rwork0.227 --
obs0.229 35551 88.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.31 Å2
Refinement stepCycle: LAST / Resolution: 3.66→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19500 100 44 0 19644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.66-3.750.39721410.36962269X-RAY DIFFRACTION84
3.75-3.850.35521340.30372442X-RAY DIFFRACTION91
3.85-3.970.36391450.29192345X-RAY DIFFRACTION87
3.97-4.090.32561370.28362353X-RAY DIFFRACTION88
4.09-4.240.32761470.25762409X-RAY DIFFRACTION89
4.24-4.410.2761450.23642417X-RAY DIFFRACTION90
4.41-4.610.2361450.21262444X-RAY DIFFRACTION90
4.61-4.850.25371420.19192435X-RAY DIFFRACTION91
4.85-5.150.3031480.20212430X-RAY DIFFRACTION90
5.16-5.550.24041450.21012438X-RAY DIFFRACTION90
5.55-6.110.27291410.22132395X-RAY DIFFRACTION89
6.11-6.990.24631390.21162410X-RAY DIFFRACTION88
6.99-8.780.21591400.19332403X-RAY DIFFRACTION88
8.78-34.380.21651370.17712375X-RAY DIFFRACTION85

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