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- PDB-6vff: Dimer of Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant... -

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Basic information

Entry
Database: PDB / ID: 6vff
TitleDimer of Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from human GLI1 gene
Components
  • Double-stranded RNA-specific editase 1
  • 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*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)
  • RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)
KeywordsHYDROLASE/RNA / protein-RNA complex / 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 / metal ion binding / nucleus / cytosol / cytoplasm
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: 2.8 Å
AuthorsThuy-boun, A.S. / 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)R01GM061115 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition.
Authors: Thuy-Boun, A.S. / Thomas, J.M. / Grajo, H.L. / Palumbo, C.M. / Park, S. / Nguyen, L.T. / Fisher, A.J. / Beal, P.A.
History
DepositionJan 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 26, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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 1.3Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Oct 11, 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: Double-stranded RNA-specific editase 1
C: 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*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)
D: RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9608
Polymers128,5094
Non-polymers1,4514
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-163 kcal/mol
Surface area42450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.000, 63.210, 142.200
Angle α, β, γ (deg.)90.000, 118.133, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 53989.715 Da / Num. of mol.: 2 / Mutation: E488Q
Source method: isolated from a genetically manipulated source
Details: N-terminal Glycine is a remnant of TEV protease cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: ADARB1, ADAR2, DRADA2, RED1 / Plasmid: pSc-ADAR / 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 CD

#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*GP*AP*UP*AP*GP*CP*UP*AP*CP*G)-3)


Mass: 10316.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: generated by solid phase oligonucleotide synthesis / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA(5-R(*CP*GP*UP*AP*GP*CP*UP*AP*UP*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3)


Mass: 10213.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 40 molecules

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


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 / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50mM MOPS pH 7.0, 20% w/v PEG 4000, 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→37.48 Å / Num. obs: 32384 / % possible obs: 97.3 % / Redundancy: 5.522 % / Biso Wilson estimate: 70.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.104 / Χ2: 0.994 / Net I/σ(I): 14.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.875.4221.1811.5622600.6111.30692.1
2.87-2.955.6690.9481.9523440.7371.04599
2.95-3.045.6730.7192.5223240.8090.79198.8
3.04-3.135.660.5653.121850.8780.62398.3
3.13-3.235.6270.3974.2621380.9170.43898.5
3.23-3.355.5830.3075.4821040.9520.33998.8
3.35-3.475.4910.2217.3819950.9740.24498.7
3.47-3.615.3220.1579.519290.9860.17498.1
3.61-3.785.370.1212.7117230.9890.13391
3.78-3.965.6560.09616.0918130.9950.10599.4
3.96-4.175.6430.08318.1816740.9960.09299.5
4.17-4.435.5810.06821.515920.9970.07598.5
4.43-4.735.4930.05525.7415340.9980.06199
4.73-5.115.4120.05825.1914020.9980.06498.2
5.11-5.65.180.05326.0312000.9970.05990.9
5.6-6.265.6250.05327.6212010.9980.05899.8
6.26-7.235.5350.04332.2310390.9990.04798.2
7.23-8.855.3090.0342.058920.9990.03498.6
8.85-12.525.2380.02253.4465010.02490.2
12.52-37.485.2440.01958.8638510.02192.8

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ED2

5ed2


Resolution: 2.8→37.48 Å / SU ML: 0.4091 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.0005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 1610 4.97 %
Rwork0.1965 30753 -
obs0.1991 32363 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6403 1357 74 36 7870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00788118
X-RAY DIFFRACTIONf_angle_d1.246611298
X-RAY DIFFRACTIONf_chiral_restr0.08331314
X-RAY DIFFRACTIONf_plane_restr0.00721200
X-RAY DIFFRACTIONf_dihedral_angle_d18.67613242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.41461240.31982453X-RAY DIFFRACTION93.03
2.88-2.980.33521330.28882554X-RAY DIFFRACTION98.93
2.98-3.080.31591260.27342573X-RAY DIFFRACTION99.16
3.08-3.20.32811370.25072577X-RAY DIFFRACTION98.08
3.2-3.350.30671310.23352609X-RAY DIFFRACTION98.99
3.35-3.530.28331300.2172584X-RAY DIFFRACTION98.58
3.53-3.750.24971370.21232418X-RAY DIFFRACTION93.15
3.75-4.040.23851320.19142593X-RAY DIFFRACTION99.6
4.04-4.440.25291230.17232629X-RAY DIFFRACTION99.21
4.44-5.080.22681570.16732597X-RAY DIFFRACTION98.64
5.08-6.40.22351400.18222539X-RAY DIFFRACTION95.78
6.4-37.480.19771400.16352627X-RAY DIFFRACTION96.31

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