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- PDB-7wkv: Crystal structure of human ALKBH5 in complex with 2-oxoglutarate ... -

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Basic information

Entry
Database: PDB / ID: 7wkv
TitleCrystal structure of human ALKBH5 in complex with 2-oxoglutarate (2OG) and m6A-containing ssRNA
Components
  • RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
  • RNA demethylase ALKBH5
KeywordsOXIDOREDUCTASE/RNA / Iron and 2-oxoglutarate dependent oxygenase / RNA demethylase / oxidoreductase / double-stranded beta helix / OXIDOREDUCTASE-RNA COMPLEX
Function / homology
Function and homology information


gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / : / oxidative RNA demethylase activity / non-membrane-bounded organelle assembly / paraspeckles / 2-oxoglutarate-dependent dioxygenase activity / mRNA destabilization ...gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / : / oxidative RNA demethylase activity / non-membrane-bounded organelle assembly / paraspeckles / 2-oxoglutarate-dependent dioxygenase activity / mRNA destabilization / mRNA export from nucleus / molecular condensate scaffold activity / mRNA processing / regulation of translation / spermatogenesis / cell differentiation / response to hypoxia / nuclear speck / Golgi apparatus / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
RNA demethylase ALKBH5 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / RNA / RNA demethylase ALKBH5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKaur, S. / McDonough, M.A. / Schofield, C.J. / Aik, W.S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)22301719 United Kingdom
Wellcome Trust106244/Z/14/Z United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Authors: Kaur, S. / Tam, N.Y. / McDonough, M.A. / Schofield, C.J. / Aik, W.S.
History
DepositionJan 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2May 4, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA demethylase ALKBH5
B: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
C: RNA demethylase ALKBH5
D: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
E: RNA demethylase ALKBH5
F: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,68912
Polymers83,0866
Non-polymers6036
Water1,60389
1
A: RNA demethylase ALKBH5
B: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8964
Polymers27,6952
Non-polymers2012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-12 kcal/mol
Surface area10960 Å2
MethodPISA
2
C: RNA demethylase ALKBH5
D: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8964
Polymers27,6952
Non-polymers2012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-11 kcal/mol
Surface area10430 Å2
MethodPISA
3
E: RNA demethylase ALKBH5
F: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8964
Polymers27,6952
Non-polymers2012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-12 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.364, 78.364, 106.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein RNA demethylase ALKBH5 / Alkylated DNA repair protein alkB homolog 5 / Alpha-ketoglutarate-dependent dioxygenase alkB homolog 5


Mass: 25138.818 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH5, ABH5, OFOXD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P6C2, mRNA N6-methyladenine demethylase
#2: RNA chain RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')


Mass: 2556.588 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.96 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) monohydrate, 16% (w/v) PEG 6000 and 5% (v/v) 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.4
ReflectionResolution: 2.1→57.29 Å / Num. obs: 42760 / % possible obs: 99.68 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.53 Å2 / CC1/2: 0.935 / Rmerge(I) obs: 0.1127 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.272 / Mean I/σ(I) obs: 1 / Num. unique obs: 4300 / CC1/2: 0.681 / % possible all: 99.07

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V4G

7v4g


Resolution: 2.1→57.26 Å / Cross valid method: THROUGHOUT / σ(F): 78.99 / Phase error: 43.59 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2275 2127 4.99 %
Rwork0.188 40528 -
obs0.1929 42646 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.37 Å2 / Biso mean: 50.5165 Å2 / Biso min: 7.43 Å2
Refinement stepCycle: final / Resolution: 2.1→57.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 267 33 89 5527
Biso mean--38.88 44.1 -
Num. residues----669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.39281230.33192659278294
2.15-2.20.3321410.29692719286095
2.2-2.260.41661650.29642663282894
2.26-2.330.28971390.26932704284394
2.33-2.40.26841360.25852702283895
2.4-2.490.30091620.2512654281694
2.49-2.590.30221230.23742760288395
2.59-2.710.26811480.23262714286295
2.71-2.850.31261570.22152640279794
2.85-3.030.27041860.2122714290093
3.03-3.260.26181280.1932703283195
3.26-3.590.20451050.18282766287196
3.59-4.110.22441560.16712694285095
4.11-5.170.17221170.1292716283396
5.18-57.260.18381320.16232720285295
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9590.86420.46250.80470.06655.002-0.0422-0.0119-0.1118-0.1804-0.0687-0.14070.36270.41380.11480.69990.14330.02380.83870.05120.219147.6233-28.220317.7981
20.48330.08040.1890.6255-0.17992.0884-0.0511-0.00630.05220.0056-0.01050.066-0.1552-0.2360.05260.74890.08370.00140.7820.00630.1334.3544-19.493918.1396
31.36910.15440.11661.53951.32081.32450.10190.15590.16060.35580.0740.1968-0.3952-0.4744-0.1780.79550.3247-0.00531.0085-0.02380.30229.7569-15.780329.0143
40.5578-0.0620.37092.36450.95471.9434-0.071-0.02340.1440.08780.001-0.1416-0.45560.11310.07220.7982-0.0258-0.02340.74340.01850.185.178913.285231.4676
51.7030.1380.63781.13030.07549.13480.1039-0.0273-0.4012-0.0934-0.11-0.03961.29770.26020.00260.74910.0758-0.0260.56580.05040.24445.9069-14.959316.8478
61.52450.19220.04421.3170.07793.08490.07210.2539-0.1477-0.2593-0.057-0.00560.51540.0217-0.00570.55330.0109-0.01580.5786-0.02820.12271.2748-6.39794.5249
75.48062.0287-0.48012.52062.46866.40230.0690.69170.5458-0.30860.09520.2787-0.8986-0.345-0.17060.55420.0646-0.01610.58170.03530.1627-3.92116.56594.8502
81.21140.0580.22611.12080.43433.57250.10310.029-0.06640.0509-0.07830.05740.2624-0.166-0.01730.4427-0.0011-0.01590.5067-0.00210.1388-2.2196-2.194717.4448
91.7734-0.30771.04542.16061.14197.69660.08140.39870.4157-0.3448-0.0003-0.3689-0.93840.8317-0.07930.6751-0.2125-0.0190.75430.01890.290513.465914.904212.2642
100.44290.56340.15061.09350.18563.45630.0022-0.07270.05690.1062-0.1026-0.0387-0.17440.20290.09160.51990.0697-0.01160.55060.01520.12712.74573.256819.3839
112.3924-0.466-1.90361.7523-0.35772.37960.08820.06470.1985-0.1482-0.0831-0.1473-0.3980.0575-0.00110.62-0.0111-0.03090.6429-0.02440.17257.64178.85236.5493
120.32280.0977-0.13381.9277-0.79771.2015-0.0777-0.1290.0339-0.12360.04160.0674-0.0139-0.01670.0290.942-0.0107-0.01980.8019-0.02520.229335.208436.1593.6063
130.78580.0918-0.19820.3614-0.23751.4395-0.0119-0.0358-0.08780.0067-0.0405-0.00040.20180.00130.03540.77980.0598-0.01160.69950.00780.075539.220716.77622.0538
140.89130.14350.46090.8006-0.14072.5021-0.0577-0.02910.10980.1008-0.0240.0458-0.3518-0.11270.06570.82120.0295-0.01710.7005-0.00410.12236.17227.700916.5256
151.04190.3287-1.08980.3292-0.13731.32850.244-0.10760.10460.4071-0.03860.0832-0.5719-0.3354-0.19490.97290.1948-0.04550.79650.05860.269232.422332.124128.3441
162.7246-0.6373-0.78161.98150.41894.54160.06850.07940.2045-0.3063-0.15320.0572-0.3297-0.20840.08460.98340.2241-0.03950.75120.00670.267531.2141-11.58125.0557
172.89140.30151.59472.7497-1.10755.63450.06220.0402-0.3914-0.0744-0.0752-0.08220.97320.14120.0141.00230.00680.08340.6971-0.04630.30835.5359-38.717218.2771
181.4953-0.0290.08071.203-0.5233.64590.0135-0.27470.01510.1838-0.0927-0.0345-0.10820.10270.06460.68780.04090.01450.73150.03190.137339.7404-25.057830.773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 150 through 188 )E150 - 188
2X-RAY DIFFRACTION2chain 'E' and (resid 189 through 292 )E189 - 292
3X-RAY DIFFRACTION3chain 'F' and (resid 2 through 5 )F2 - 5
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 93 )A74 - 93
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 115 )A94 - 115
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 135 )A116 - 135
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 149 )A136 - 149
8X-RAY DIFFRACTION8chain 'A' and (resid 150 through 228 )A150 - 228
9X-RAY DIFFRACTION9chain 'A' and (resid 229 through 243 )A229 - 243
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 292 )A244 - 292
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 5 )B2 - 5
12X-RAY DIFFRACTION12chain 'C' and (resid 74 through 93 )C74 - 93
13X-RAY DIFFRACTION13chain 'C' and (resid 94 through 205 )C94 - 205
14X-RAY DIFFRACTION14chain 'C' and (resid 206 through 292 )C206 - 292
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 5 )D2 - 5
16X-RAY DIFFRACTION16chain 'E' and (resid 74 through 93 )E74 - 93
17X-RAY DIFFRACTION17chain 'E' and (resid 94 through 115 )E94 - 115
18X-RAY DIFFRACTION18chain 'E' and (resid 116 through 149 )E116 - 149

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