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- PDB-4nro: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 4nro
TitleCrystal structure of human ALKBH5 in complex with alpha-ketoglutarate
ComponentsRNA demethylase ALKBH5
KeywordsOXIDOREDUCTASE / alkbh5 / 6-methyl adenosine / PROTEIN/DNA INTERACTION / HUMAN DIOXYGENASE / METAL-BINDING / NUCLEUS / demethylation / RNA REPAIR
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 / regulation of mRNA export from nucleus / regulation of mRNA processing / paraspeckles / membraneless organelle assembly / 2-oxoglutarate-dependent dioxygenase activity ...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 / regulation of mRNA export from nucleus / regulation of mRNA processing / paraspeckles / membraneless organelle assembly / 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 / nucleus / metal ion binding / cytosol
Similarity search - Function
RNA demethylase ALKBH5 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / RNA demethylase ALKBH5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFeng, C. / Chen, Z. / Liu, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition
Authors: Feng, C. / Liu, Y. / Wang, G. / Deng, Z. / Zhang, Q. / Wu, W. / Tong, Y. / Cheng, C. / Chen, Z.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5863
Polymers26,3851
Non-polymers2012
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.177, 56.177, 144.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 26385.127 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 66-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABH5, ALKBH5, OFOXD1 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P6C2, 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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 289 K / pH: 5
Details: 20% PEG 4K, 100mM CH3CO2NH4, 100mM Na-citrate , pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9906 / % possible obs: 90 % / Observed criterion σ(I): 3
Reflection shellResolution: 2.3→2.34 Å / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NRM

4nrm


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.902 / SU B: 14.714 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 473 4.8 %RANDOM
Rwork0.23735 ---
obs0.2383 9363 89.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.809 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å2-0 Å2
2--1.36 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 11 110 1690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.9592208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.17122.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18315230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0931511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211243
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9194.512851
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0766.7481061
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0484.56775
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.60431608
X-RAY DIFFRACTIONr_sphericity_free21.18754
X-RAY DIFFRACTIONr_sphericity_bonded16.2851576
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 41 -
Rwork0.242 693 -
obs--91.18 %
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)
12.9921.65664.5421.31911.8378.0889-0.00810.07820.0468-0.01980.18910.13340.0166-0.115-0.1810.0565-0.00380.00040.06650.02070.1239-2.305828.76883.8681
25.69911.35730.02741.3820.23170.0579-0.13450.10140.2303-0.05790.09180.1621-0.03080.01280.04280.11180.0014-0.01570.00660.00720.08915.959239.034118.0722
30.9737-1.42380.3413.7111-0.74931.4331-0.0597-0.14850.1140.03730.1101-0.246-0.0930.1154-0.05040.0332-0.0156-0.0170.0702-0.03070.100727.420925.47225.7538
40.2552-1.1187-0.41514.95721.83220.67820.05840.0067-0.0283-0.2487-0.09060.0674-0.0935-0.02430.03220.03170.0046-0.01430.1140.03010.093122.009613.304120.6523
52.54861.0012-1.63051.2355-1.35651.6682-0.1515-0.0002-0.0590.00590.1256-0.08090.0346-0.13760.02590.01330.0070.01090.10880.0270.160516.49516.081225.1527
68.59022.05017.13491.03341.85495.97380.07340.1669-0.20670.20410.04770.04050.10480.1549-0.12110.0729-0.00640.00370.06980.05140.11529.84810.110628.1092
70.9795-0.41580.02561.09840.11530.0215-0.0513-0.11160.11080.03110.0478-0.0611-0.016100.00350.077-0.0003-0.0090.0649-0.03020.054615.495628.661526.0726
81.12030.0931-1.62750.0105-0.12452.56490.0138-0.0411-0.1071-0.00070.0112-0.02340.06440.086-0.0250.1147-0.0122-0.02670.0516-0.03930.20716.447516.80217.9882
90.9164-0.5928-0.25350.38390.17050.2298-0.00210.02720.0351-0.0037-0.0191-0.018-0.12830.00040.02110.1151-0.01250.00350.0573-0.00540.083713.582428.750717.4948
100.81580.7327-1.11860.6875-1.03911.5749-0.05710.1726-0.0051-0.01330.12280.05260.0406-0.1878-0.06570.10050.0260.03170.207-0.1360.14968.267718.1222.5021
113.00942.68692.98286.81136.7196.7063-0.16720.330.241-0.2152-0.01660.1683-0.24140.06470.18370.0979-0.00820.00560.08750.02130.02677.978625.51511.815
120.661-0.26830.49780.3431-0.40450.5528-0.04830.07530.01810.01790.05280.0037-0.049-0.0163-0.00440.07630.00240.02520.0581-0.03040.09489.75125.997311.1974
132.07920.2580.83080.28110.20290.37550.0631-0.1403-0.03620.0158-0.0156-0.07370.0093-0.0564-0.04760.09780.00010.03450.0477-0.01830.057111.928821.775322.9035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A73 - 90
2X-RAY DIFFRACTION2A91 - 97
3X-RAY DIFFRACTION3A98 - 121
4X-RAY DIFFRACTION4A122 - 130
5X-RAY DIFFRACTION5A131 - 141
6X-RAY DIFFRACTION6A142 - 160
7X-RAY DIFFRACTION7A161 - 200
8X-RAY DIFFRACTION8A201 - 211
9X-RAY DIFFRACTION9A212 - 225
10X-RAY DIFFRACTION10A226 - 237
11X-RAY DIFFRACTION11A238 - 248
12X-RAY DIFFRACTION12A249 - 273
13X-RAY DIFFRACTION13A274 - 292

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