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- PDB-4oct: Crystal structure of human ALKBH5 crystallized in the presence of... -

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Basic information

Entry
Database: PDB / ID: 4oct
TitleCrystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate
ComponentsRNA demethylase ALKBH5
KeywordsOXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC / RNA demethylase
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 / paraspeckles / non-membrane-bounded organelle assembly / 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 / paraspeckles / non-membrane-bounded 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 / direct placement / Resolution: 2.28 Å
AuthorsTempel, W. / Chao, X. / Liu, K. / Dong, A. / Cerovina, T. / He, H. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation.
Authors: Xu, C. / Liu, K. / Tempel, W. / Demetriades, M. / Aik, W. / Schofield, C.J. / Min, J.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _diffrn_source.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA demethylase ALKBH5
B: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,08029
Polymers50,6782
Non-polymers40227
Water41423
1
A: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,54012
Polymers25,3391
Non-polymers20111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,54017
Polymers25,3391
Non-polymers20116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.930, 57.234, 78.407
Angle α, β, γ (deg.)90.000, 101.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 77 - 293 / Label seq-ID: 5 - 221

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 25339.010 Da / Num. of mol.: 2 / Fragment: UNP residues 74-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH5, ABH5, OFOXD1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 23 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.005 M of each manganous sulfate and 2-oxyglutarate were added to the protein stock solution. Reservoir: 20% PEG-3350, 0.2 M diammonium phosphate, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→38.47 Å / Num. obs: 18808 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 13.3
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
2.28-2.367.12.1131931848100
8.83-38.476.652.5229934898.9

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: direct placement
Starting model: related to pdb entry 4O61

4o61


Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2464 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.686 / SU B: 27.978 / SU ML: 0.305 / SU R Cruickshank DPI: 0.4723 / SU Rfree: 0.2846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.472 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: PDB entry 2IUW aided in the interpretation of the manganese cation binding site. Coot was used for interactive model adjustments. Molprobity was used for validation of model geometry.
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 934 5 %THIN SHELLS (SFTOOLS)
Rwork0.2382 ---
obs0.2405 18790 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.63 Å2 / Biso mean: 45.2232 Å2 / Biso min: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å2-0 Å20.85 Å2
2--1.87 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 45 23 3316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193360
X-RAY DIFFRACTIONr_bond_other_d0.0040.023154
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9674547
X-RAY DIFFRACTIONr_angle_other_deg0.87837239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.91523.113151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77515541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841529
X-RAY DIFFRACTIONr_chiral_restr0.0770.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02758
X-RAY DIFFRACTIONr_mcbond_it0.9351.2321677
X-RAY DIFFRACTIONr_mcbond_other0.9351.2321676
X-RAY DIFFRACTIONr_mcangle_it1.5591.8422091
Refine LS restraints NCS

Ens-ID: 1 / Number: 12076 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 53 -
Rwork0.301 1326 -
all-1379 -
obs--100 %
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)
10.81120.04091.07223.07830.58693.13890.0197-0.1553-0.0739-0.26350.0206-0.02750.0127-0.3809-0.04020.40330.0092-0.13430.42190.03380.060816.10475.02886.1494
21.62380.56111.04383.23580.36521.3874-0.0484-0.0980.06480.18020.0838-0.1413-0.04950.1132-0.03540.39040.0077-0.13570.4360.00610.064529.59050.666839.3732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 502
2X-RAY DIFFRACTION2B76 - 502

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