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- PDB-5ed1: Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bo... -

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Basic information

Entry
Database: PDB / ID: 5ed1
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from S. cerevisiae BDF2 gene
Components
  • Double-stranded RNA-specific editase 1
  • RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3')
  • RNA (5'-R(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3')
KeywordsHYDROLASE/RNA / deaminase / human / 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 neuron apoptotic process / motor behavior / 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 / mRNA binding / innate immune response / 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)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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)R01GM061115 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity.
Authors: Matthews, M.M. / Thomas, J.M. / Zheng, Y. / Tran, K. / Phelps, K.J. / Scott, A.I. / Havel, J. / Fisher, A.J. / Beal, P.A.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 14, 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 1.6Feb 10, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression
Revision 1.7Sep 27, 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(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3')
C: RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3')
D: Double-stranded RNA-specific editase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1758
Polymers104,7244
Non-polymers1,4514
Water59433
1
A: Double-stranded RNA-specific editase 1
B: RNA (5'-R(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3')
C: RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3')
hetero molecules

D: Double-stranded RNA-specific editase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1758
Polymers104,7244
Non-polymers1,4514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area9500 Å2
ΔGint-148 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.362, 107.498, 121.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Double-stranded RNA-specific editase 1 / adenosine deaminase acting on RNA


Mass: 45004.398 Da / Num. of mol.: 2 / Fragment: A to I editase (UNP residues 327-729) / Mutation: E488Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 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(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3')


Mass: 7225.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: RNA chain RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3')


Mass: 7489.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 3 types, 37 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.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 55.1 % / Description: cube-like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/NaOH, pH 6.5, 9% w/v PEG3350, 13% glycerol, 0.015 M NAD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 24, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→100 Å / Num. obs: 27727 / % possible obs: 96.5 % / Redundancy: 2.93 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.57
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.52 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692phasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZY7

1zy7


Resolution: 2.77→80.392 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1352 4.98 %
Rwork0.1627 --
obs0.1659 27153 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→80.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6197 973 74 33 7277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017492
X-RAY DIFFRACTIONf_angle_d1.34210365
X-RAY DIFFRACTIONf_dihedral_angle_d15.8262950
X-RAY DIFFRACTIONf_chiral_restr0.0521195
X-RAY DIFFRACTIONf_plane_restr0.0071151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.8690.30491220.25292602X-RAY DIFFRACTION99
2.869-2.98390.31751260.24062601X-RAY DIFFRACTION99
2.9839-3.11970.31721280.23212554X-RAY DIFFRACTION97
3.1197-3.28420.27251340.19692579X-RAY DIFFRACTION98
3.2842-3.48990.2581380.17952596X-RAY DIFFRACTION99
3.4899-3.75940.23611220.16752597X-RAY DIFFRACTION98
3.7594-4.13770.21831510.14582522X-RAY DIFFRACTION96
4.1377-4.73640.19431390.12752581X-RAY DIFFRACTION97
4.7364-5.96710.18011360.14492576X-RAY DIFFRACTION95
5.9671-80.42620.19961560.14682593X-RAY DIFFRACTION92
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)
18.96289.47855.13052.00147.52362.0067-0.5714-0.07731.4697-0.0854-0.3554-0.2389-0.1182-0.35460.92020.8983-0.0107-0.18050.95460.04980.497-24.8184-19.928616.8133
22.6742-0.26970.88194.15921.34133.41350.0708-0.12780.051-0.1072-0.23810.85980.4292-0.97340.15490.3546-0.09590.02280.62120.07530.4068-24.9089-22.456539.9318
32.4304-1.51910.05547.99040.22162.17720.05310.0082-0.5182-0.32890.02230.83220.6188-0.5003-0.09240.4919-0.2224-0.01310.54640.0480.3362-19.0317-29.785232.3149
44.5291-2.028-0.32988.3295-1.97219.2631-0.14440.45360.3843-0.51450.34450.5178-0.0078-0.1626-0.25940.3948-0.0771-0.0260.30460.11130.3961-12.7537-2.385529.3692
51.11250.35380.8442.72670.0472.9331-0.10120.09960.0599-0.38010.14410.1596-0.0575-0.2972-0.03820.2658-0.05440.01220.33230.03350.2651-12.4973-17.912930.7696
62.5158-1.9135-0.06933.37991.60883.8027-0.1854-0.3986-0.27740.21230.22110.51320.3072-0.66380.00020.4187-0.07580.07080.53080.0960.4063-18.2264-23.911548.8138
72.5428-0.55271.35063.8573-0.83725.61680.03350.1881-0.1412-0.0164-0.1-0.26540.70650.1660.08690.3050.02530.04770.3918-0.00960.3672-0.1579-23.769137.4308
84.8325-0.2214-0.03021.90810.56266.5539-0.1450.86370.2852-0.5990.07450.0926-0.50070.24260.05530.6882-0.0368-0.14310.40320.05140.428-7.3194-45.3035-1.5402
96.5286-2.36512.46622.2477-1.30033.21930.11750.71570.6153-0.9109-0.37890.3053-0.4202-0.45730.23610.80090.0992-0.26040.6557-0.02920.521-17.6287-45.0325-8.2264
100.4024-1.6032-0.06057.75852.47473.6428-0.17240.1678-0.4435-1.9091-0.39630.88460.967-0.40150.51481.7616-0.1179-0.25130.7069-0.21531.1612-4.0932-76.1758-4.7161
113.29662.37990.47271.7450.63812.73040.8938-0.1528-1.23361.17130.2454-0.58642.3690.6047-1.11482.32950.0989-0.5681.1112-0.34061.2469-10.543-82.31160.131
128.40432.3411-1.91996.5196-0.972.06730.0896-0.6393-0.41661.0365-0.0491-0.23250.26250.303-0.05990.56480.012-0.04080.42030.01780.4628-10.6391-63.617912.5074
135.6953-0.7058-0.97882.79370.74632.6575-0.00030.1699-0.1593-0.0111-0.24540.38070.1889-0.32350.31470.5767-0.0371-0.20560.4064-0.08230.4373-16.1711-55.82593.303
142.7365-0.41770.38072.82850.91283.6298-0.066-0.11420.253-0.3397-0.24090.6474-0.5821-0.95680.29490.52010.1011-0.19940.5651-0.04490.5442-20.8011-48.25674.232
157.284-5.3586-3.84489.38865.32297.78881.6581-1.23850.8295-0.073-1.58330.14210.3523-1.0945-0.06361.0845-0.2105-0.09740.6077-0.06520.516-12.00078.219617.7963
166.3932.73796.10552.00671.0566.0601-0.1919-0.54220.7720.84820.23790.7259-0.71011.3787-0.11521.2131-0.10950.10840.8025-0.08120.7874-17.76416.7429.0435
177.7771-0.4433.02468.3302-2.59419.2535-0.05370.11790.71650.20750.47010.5913-1.31-1.2643-0.25640.53630.140.13150.56840.10940.4982-22.33510.81239.8303
181.34731.4884-1.58494.3392.43718.4442-0.0244-0.23390.31852.0996-0.16071.5619-1.2681-0.76630.13541.16950.36970.28890.993-0.00960.7526-25.75855.393258.1944
196.60581.5461-1.09277.36177.48658.74481.04751.48970.7752-1.078-0.23410.3773-0.4833-2.0112-0.80471.41730.20850.18781.42490.16230.6736-34.7884-7.115364.5784
207.7242-4.32386.01849.1414-4.79719.39781.02711.5350.4277-1.9912-1.1428-0.4609-1.28150.63070.09241.34660.08340.19621.43180.01420.6267-25.3983-7.921662.8814
214.4841-1.42453.14786.8647-9.07332.01060.53661.46570.7522-0.66661.68071.26520.0583-2.4432-2.18391.41490.70.23362.03510.41560.8831-31.41883.67552.0829
222.0144.35145.61047.2833-3.7092.0055-0.0298-0.9311.3690.0841-0.00981.1439-1.5667-1.00680.05410.70070.16320.130.57990.01330.6792-16.90167.858544.0085
234.9658-3.21363.96285.815-5.95888.36620.17090.03920.8237-0.73060.33141.1779-0.8648-0.9258-0.50060.88220.1759-0.14060.6310.25720.7419-19.88488.450126.1642
248.2566-4.4943-0.35888.39485.2084.5835-0.5180.9491.21780.1730.731-0.1679-0.1871-0.8286-0.23811.5551-0.155-0.00690.68840.10910.7188-12.977917.019814.9487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 305:315)
2X-RAY DIFFRACTION2(chain A and resid 316:405)
3X-RAY DIFFRACTION3(chain A and resid 406:466)
4X-RAY DIFFRACTION4(chain A and resid 467:497)
5X-RAY DIFFRACTION5(chain A and resid 498:587)
6X-RAY DIFFRACTION6(chain A and resid 588:644)
7X-RAY DIFFRACTION7(chain A and resid 645:700)
8X-RAY DIFFRACTION8(chain D and resid 304:405)
9X-RAY DIFFRACTION9(chain D and resid 406:462)
10X-RAY DIFFRACTION10(chain D and resid 463:468)
11X-RAY DIFFRACTION11(chain D and resid 469:475)
12X-RAY DIFFRACTION12(chain D and resid 476:496)
13X-RAY DIFFRACTION13(chain D and resid 497:562)
14X-RAY DIFFRACTION14(chain D and resid 563:700)
15X-RAY DIFFRACTION15(chain B and resid 1:4)
16X-RAY DIFFRACTION16(chain B and resid 5:8)
17X-RAY DIFFRACTION17(chain B and resid 9:14)
18X-RAY DIFFRACTION18(chain B and resid 15:19)
19X-RAY DIFFRACTION19(chain B and resid 20:23)
20X-RAY DIFFRACTION20(chain C and resid 1:4)
21X-RAY DIFFRACTION21(chain C and resid 5:9)
22X-RAY DIFFRACTION22(chain C and resid 10:13)
23X-RAY DIFFRACTION23(chain C and resid 14:19)
24X-RAY DIFFRACTION24(chain C and resid 20:23)

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