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- PDB-7v4g: Crystal structure of human ALKBH5 in complex with m6A-containing ssRNA -

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Basic information

Entry
Database: PDB / ID: 7v4g
TitleCrystal structure of human ALKBH5 in complex with 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 / 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
: / 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
DepositionAug 13, 2021Deposition 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
D: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
E: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
F: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
A: RNA demethylase ALKBH5
B: RNA demethylase ALKBH5
C: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,90816
Polymers83,0866
Non-polymers82110
Water4,234235
1
D: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
A: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0316
Polymers27,6952
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-37 kcal/mol
Surface area10300 Å2
MethodPISA
2
E: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
B: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0316
Polymers27,6952
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-37 kcal/mol
Surface area10330 Å2
MethodPISA
3
F: RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
C: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8464
Polymers27,6952
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-31 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.474, 76.474, 106.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

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RNA chain / Protein , 2 types, 6 molecules DEFABC

#1: 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)
#2: 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

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Non-polymers , 4 types, 245 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium sulfate decahydrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→41.46 Å / Num. obs: 40605 / % possible obs: 99.97 % / Redundancy: 5 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.2107 / Net I/σ(I): 8.61
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 1.121 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4132 / CC1/2: 0.536

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
GDAdata collection
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NJ4

4nj4


Resolution: 2.1→41.46 Å / Cross valid method: THROUGHOUT / σ(F): 322.43 / Phase error: 34.54 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2236 2017 4.97 %
Rwork0.1851 38584 -
obs0.1905 40601 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.65 Å2 / Biso mean: 30.9377 Å2 / Biso min: 13.95 Å2
Refinement stepCycle: final / Resolution: 2.1→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 267 42 235 5564
Biso mean--28.2 28.67 -
Num. residues----652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.25251320.23392766289895
2.15-2.210.2761040.22572792289696
2.21-2.280.27491600.22782778293895
2.28-2.350.24261220.22622746286896
2.35-2.430.28931840.21492731291594
2.43-2.530.2661920.20622702289493
2.53-2.650.251520.20562741289395
2.65-2.790.22671300.19792803293396
2.79-2.960.22941290.19152725285495
2.96-3.190.21211370.17842770290795
3.19-3.510.22321810.17292719290094
3.51-4.020.22761320.17342789292195
4.02-5.060.17711400.15942754289495
5.06-41.460.20691220.18992768289096
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)
10.8238-0.1006-0.31311.0319-0.4522.3788-0.017-0.0544-0.0845-0.06160.0442-0.04720.39930.0664-0.03260.2980.0311-0.01780.2306-0.00880.076444.003919.260617.9243
21.52540.29240.38971.5967-0.19022.30810.2413-0.1531-0.0864-0.4494-0.08310.12380.8676-0.4242-0.18670.594-0.0629-0.07450.458-0.00530.207132.5766-26.6889-2.6188
31.04970.38880.34461.3623-0.64241.83120.3749-0.53-0.29280.3839-0.22760.01470.8858-0.4843-0.14030.5594-0.1299-0.10830.54550.03250.267136.0541-27.980215.8332
41.9962-0.8104-0.37593.4609-0.33360.9247-0.1784-0.05460.19870.48870.5834-0.39690.264-0.0704-0.44340.5116-0.0257-0.06460.5052-0.00760.222744.7943-16.696115.1507
55.11052.1621.41954.4545-0.85662.43540.01130.1947-0.4370.11420.2679-0.3010.76830.361-0.28790.73110.0569-0.12590.3318-0.05650.322642.5407-35.54616.105
60.5260.2246-0.87830.3115-0.61191.7269-0.10340.3865-0.5564-0.55120.5218-0.49170.78870.5354-0.28540.72270.2007-0.01530.6943-0.23450.380144.796-30.9529-6.5007
71.37660.1405-0.34871.7976-0.74411.79370.2602-0.1709-0.01320.16370.02590.1115-0.018-0.0703-0.27120.4248-0.0632-0.01560.41730.01480.200235.0442-20.29163.7127
81.096-1.1144-0.17651.83640.41140.93160.0214-0.09770.0288-0.15630.17850.27750.1215-0.6792-0.19830.3898-0.0175-0.01510.65340.09320.208227.4741-13.28191.7051
91.4543-0.6142-0.34661.8837-0.71354.12890.2232-0.30350.0316-0.14680.05590.1404-0.02760.0614-0.28810.3285-0.06410.0130.37140.00190.196237.158-18.20153.3997
100.3234-0.2079-0.19881.557-0.03340.1415-0.0021-0.0561-0.26980.03690.13470.04840.3756-0.0518-0.05910.3351-0.0139-0.05210.2518-0.0070.1589-2.0572-12.117124.1252
111.98220.66851.59224.97563.13382.776-0.14320.2986-0.2546-0.2590.4762-0.1602-0.02030.7311-0.22970.40990.0480.00710.35450.01690.122349.710417.71827.2971
122.36981.64150.1421.78050.16840.01570.1848-0.85290.051-0.0131-0.19540.2142-0.36550.19540.12960.370.0601-0.03450.5630.02110.164530.7882-12.930513.945
133.16411.70320.09241.78930.59591.42510.00640.03640.1247-0.1888-0.03020.13420.09870.04510.02060.35090.0744-0.00140.29790.0190.0928-0.6072-5.85820.2451
140.29460.4447-0.21921.1733-0.60031.6527-0.0737-0.30150.00170.0598-0.0015-0.23810.11480.7153-0.1130.2377-0.04280.00390.574-0.0706-0.025810.86032.913821.6179
151.52340.89211.86044.69441.52933.1241-0.0293-0.0605-0.07850.3210.14790.27470.2295-0.4222-0.09290.32010.08620.01120.2839-0.02490.063-7.163-1.269425.6972
161.2534-0.2676-0.01581.17880.31312.17670.15510.16770.1918-0.04090.0332-0.1222-0.51750.2292-0.19140.2934-0.01010.03080.2466-0.02590.11091.32749.631313.2633
170.7604-0.1863-0.03921.1368-0.14341.8386-0.0133-0.0193-0.0708-0.03930.0704-0.02870.22040.1672-0.05950.23620.01110.00250.2347-0.00810.0785-0.4433-6.542313.3561
180.2093-0.45730.07871.3109-0.36332.08350.0406-0.0992-0.1143-0.12840.11170.06420.6088-0.3529-0.15240.3657-0.1169-0.00730.34610.04140.043834.851415.906316.4627
192.919-1.0865-0.222.31670.83461.98830.24670.01890.2744-0.1944-0.0487-0.3364-0.52620.0858-0.1090.3593-0.022-0.01730.231-0.01380.111843.038927.76475.5122
200.2879-0.42290.22380.82260.12792.4956-0.0459-0.07740.06170.11440.16750.1482-0.18-0.6998-0.05780.29240.0152-0.01420.39150.05710.077329.390526.030118.1035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 189 through 292 )B189 - 292
2X-RAY DIFFRACTION2chain 'C' and (resid 79 through 115 )C79 - 115
3X-RAY DIFFRACTION3chain 'C' and (resid 116 through 135 )C116 - 135
4X-RAY DIFFRACTION4chain 'C' and (resid 136 through 159 )C136 - 159
5X-RAY DIFFRACTION5chain 'C' and (resid 160 through 171 )C160 - 171
6X-RAY DIFFRACTION6chain 'C' and (resid 172 through 188 )C172 - 188
7X-RAY DIFFRACTION7chain 'C' and (resid 189 through 228 )C189 - 228
8X-RAY DIFFRACTION8chain 'C' and (resid 229 through 256 )C229 - 256
9X-RAY DIFFRACTION9chain 'C' and (resid 257 through 292 )C257 - 292
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 5 )D2 - 5
11X-RAY DIFFRACTION11chain 'E' and (resid 2 through 5 )E2 - 5
12X-RAY DIFFRACTION12chain 'F' and (resid 2 through 5 )F2 - 5
13X-RAY DIFFRACTION13chain 'A' and (resid 81 through 96 )A81 - 96
14X-RAY DIFFRACTION14chain 'A' and (resid 97 through 135 )A97 - 135
15X-RAY DIFFRACTION15chain 'A' and (resid 136 through 149 )A136 - 149
16X-RAY DIFFRACTION16chain 'A' and (resid 150 through 188 )A150 - 188
17X-RAY DIFFRACTION17chain 'A' and (resid 189 through 292 )A189 - 292
18X-RAY DIFFRACTION18chain 'B' and (resid 79 through 135 )B79 - 135
19X-RAY DIFFRACTION19chain 'B' and (resid 136 through 149 )B136 - 149
20X-RAY DIFFRACTION20chain 'B' and (resid 150 through 188 )B150 - 188

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