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- PDB-6d06: Human ADAR2d E488Y mutant complexed with dsRNA containing an abas... -

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Basic information

Entry
Database: PDB / ID: 6d06
TitleHuman ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base
Components
  • Double-stranded RNA-specific editase 1
  • RNA (5'-R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
  • RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
KeywordsHYDROLASE/RNA / adenosine deaminase / RNA editing / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation ...hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / neuromuscular process controlling posture / adenosine to inosine editing / neuromuscular synaptic transmission / innervation / motor behavior / motor neuron apoptotic process / positive regulation of viral genome replication / RNA processing / negative regulation of cell migration / multicellular organism growth / mRNA processing / double-stranded RNA binding / defense response to virus / regulation of cell cycle / negative regulation of cell population proliferation / innate immune response / mRNA binding / synapse / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
ADAR2, first double-stranded RNA binding domain / ADAR2, second double-stranded RNA binding domain / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Double-stranded RNA binding motif / Cytokine IL1/FGF / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMatthews, M.M. / Fisher, A.J. / Beal, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM061115 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: A Bump-Hole Approach for Directed RNA Editing.
Authors: Monteleone, L.R. / Matthews, M.M. / Palumbo, C.M. / Thomas, J.M. / Zheng, Y. / Chiang, Y. / Fisher, A.J. / Beal, P.A.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 2.0Jan 1, 2020Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code / _pdbx_audit_support.funding_organization
Revision 2.1Sep 30, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _struct_conn.conn_type_id ..._chem_comp.pdbx_synonyms / _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.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-specific editase 1
B: RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
C: RNA (5'-R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
D: Double-stranded RNA-specific editase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1728
Polymers104,7214
Non-polymers1,4514
Water86548
1
A: Double-stranded RNA-specific editase 1
B: RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
C: RNA (5'-R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4075
Polymers59,6813
Non-polymers7252
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-88 kcal/mol
Surface area22300 Å2
MethodPISA
2
D: Double-stranded RNA-specific editase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7653
Polymers45,0391
Non-polymers7252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-51 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.680, 63.440, 132.060
Angle α, β, γ (deg.)90.00, 126.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Double-stranded RNA-specific editase 1 / RNA-editing deaminase 1 / RNA-editing enzyme 1 / dsRNA adenosine deaminase


Mass: 45039.445 Da / Num. of mol.: 2 / Mutation: E488Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADARB1, ADAR2, DRADA2, RED1 / Plasmid: pSc / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123
References: UniProt: P78563, double-stranded RNA adenine deaminase

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RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')


Mass: 7415.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')


Mass: 7226.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 52 molecules

#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.6 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES:NaOH pH 6.5, 14% PEG 20,000 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.55→106 Å / Num. obs: 37329 / % possible obs: 97.4 % / Redundancy: 3.44 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.27
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 2749 / CC1/2: 0.736 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZY7

1zy7


Resolution: 2.55→105.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.895 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25518 1862 5 %RANDOM
Rwork0.19012 ---
obs0.19334 35463 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å21.2 Å2
2---4.83 Å20 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.55→105.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5760 967 74 48 6849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0187069
X-RAY DIFFRACTIONr_bond_other_d0.0020.026052
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.8669796
X-RAY DIFFRACTIONr_angle_other_deg1.1013.00114068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1665738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14322.902255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.634151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4781550
X-RAY DIFFRACTIONr_chiral_restr0.0890.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217069
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021473
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_it4.6986.4772955
X-RAY DIFFRACTIONr_mcbond_other4.6956.4752954
X-RAY DIFFRACTIONr_mcangle_it7.0029.7043689
X-RAY DIFFRACTIONr_mcangle_other7.0019.7063690
X-RAY DIFFRACTIONr_scbond_it4.8176.6894113
X-RAY DIFFRACTIONr_scbond_other4.8156.6874109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0559.9236101
X-RAY DIFFRACTIONr_long_range_B_refined9.17172.5617956
X-RAY DIFFRACTIONr_long_range_B_other9.17172.5667957
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 135 -
Rwork0.308 2610 -
obs--98.21 %

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