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- PDB-4nj4: Crystal Structure of Human ALKBH5 -

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Basic information

Entry
Database: PDB / ID: 4nj4
TitleCrystal Structure of Human ALKBH5
ComponentsRNA demethylase ALKBH5
KeywordsOxidoreductase/Oxidoreductase inhibitor / double-stranded beta helix / jelly-roll motif / dioxygenase / RNA demethylase / RNA / Oxidoreductase-Oxidoreductase inhibitor 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 / 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
: / NITRATE ION / Chem-UN9 / RNA demethylase ALKBH5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsAik, W.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation.
Authors: Aik, W. / Scotti, J.S. / Choi, H. / Gong, L. / Demetriades, M. / Schofield, C.J. / McDonough, M.A.
History
DepositionNov 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 21, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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)58,63112
Polymers57,4972
Non-polymers1,13410
Water4,017223
1
A: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3306
Polymers28,7491
Non-polymers5825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA demethylase ALKBH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3006
Polymers28,7491
Non-polymers5525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 82.660, 89.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

DetailsAUTHORS ALSO STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28748.676 Da / Num. of mol.: 2 / Fragment: ALKBH5 residues 66-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABH5, ALKBH5, OFOXD1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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

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Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UN9 / N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE


Mass: 280.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE STARTING COMPOUND USED FOR CRYSTALLIZATION HAS A CHLORINE ATOM ON POSITION C7 WHICH IS ...THE STARTING COMPOUND USED FOR CRYSTALLIZATION HAS A CHLORINE ATOM ON POSITION C7 WHICH IS DEPARTING ATOM UPON REACTION WITH CYS 200 (SEE LINK RECORDS REMARK)

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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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 3350, 0.125 M potassium nitrate, 0.5 mM manganese (II) chloride, 2 mM UN9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97889 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2013 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 33289 / Num. obs: 33274 / % possible obs: 99.955 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 30.22 Å2 / Rmerge(I) obs: 0.142 / Χ2: 1.139 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allΧ2% possible allRmerge(I) obs
2.02-2.095.6232791.186100
2.09-2.186332801.2061000.781
2.18-2.276432391.25899.80.571
2.27-2.395.9533001.20299.90.438
2.39-2.545.66.333001.1821000.334
2.54-2.746.27.532921.1241000.262
2.74-3.025.99.633271.11000.19
3.02-3.456.412.233401.0471000.135
3.45-4.356.113.933791.00399.90.105
4.35-50616.535381.11499.90.09

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB entries 4IE5, 3S57, 2IUW, and 3THT

4ie5

3s57

2iuw

3tht


Resolution: 2.02→44.99 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2004 -6% random
Rwork0.1646 ---
obs-33233 94 %-
Displacement parametersBiso max: 112.13 Å2 / Biso mean: 40.5322 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: LAST / Resolution: 2.02→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 68 223 3623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_deg1.19
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.017-2.06740.30491380.2658X-RAY DIFFRACTION223094.7
4.8593-44.99320.19991490.1657X-RAY DIFFRACTION254899.6

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