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- PDB-5hp3: Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA ... -

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Basic information

Entry
Database: PDB / ID: 5hp3
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA sequence derived from S. cerevisiae BDF2 gene with AC mismatch at reaction site
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 / adenosine to inosine editing / 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 / adenosine to inosine editing / negative regulation of protein kinase activity by regulation of protein phosphorylation / double-stranded RNA adenosine deaminase activity / base conversion or substitution editing / neuromuscular process controlling posture / adenosine deaminase activity / 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 / innate immune response / mRNA binding / synapse / nucleolus / RNA binding / nucleoplasm / metal ion binding / identical protein 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) / Cytokine IL1/FGF / Double-stranded RNA binding motif / 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: 3.091 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
DepositionJan 20, 2016Deposition 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)106,1778
Polymers104,7264
Non-polymers1,4514
Water181
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)106,1778
Polymers104,7264
Non-polymers1,4514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area9570 Å2
ΔGint-146 kcal/mol
Surface area38270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.510, 107.210, 120.620
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 / RNA-editing deaminase 1 / RNA-editing enzyme 1 / dsRNA adenosine deaminase


Mass: 45005.383 Da / Num. of mol.: 2 / Fragment: UNP residues 299-701
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(*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, 5 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.: 1 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG3350, 15% glycerol, 0.1 M MES/NaOH, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.09→80.14 Å / Num. obs: 19369 / % possible obs: 96.8 % / Redundancy: 3.31 % / CC1/2: 0.993 / Rmerge(I) obs: 0.116 / Net I/σ(I): 10.56
Reflection shellResolution: 3.09→3.17 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 1.75 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZY7

1zy7


Resolution: 3.091→36.327 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.2379 988 5.11 %
Rwork0.1629 --
obs0.1668 19325 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.091→36.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6157 973 74 1 7205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017451
X-RAY DIFFRACTIONf_angle_d1.36510314
X-RAY DIFFRACTIONf_dihedral_angle_d15.7372925
X-RAY DIFFRACTIONf_chiral_restr0.0551193
X-RAY DIFFRACTIONf_plane_restr0.0071144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0912-3.25410.34551300.2522494X-RAY DIFFRACTION94
3.2541-3.45780.30891370.21222589X-RAY DIFFRACTION97
3.4578-3.72450.23411240.18142634X-RAY DIFFRACTION99
3.7245-4.09890.25831580.16012623X-RAY DIFFRACTION98
4.0989-4.69090.23131370.13682630X-RAY DIFFRACTION97
4.6909-5.90590.21561440.14422673X-RAY DIFFRACTION98
5.9059-36.32910.19981580.14852694X-RAY DIFFRACTION95
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)
10.00050.01080.00540.0918-0.03480.0511-0.3902-0.1645-0.5194-0.4204-0.01480.4431-0.7208-0.5109-0.00420.95010.17920.02251.21550.06440.6675-24.4272-21.56716.7664
20.7852-0.5135-0.44511.3833-0.36890.76140.37410.17830.5658-0.4385-0.440.61030.5261-1.0418-0.03850.307-0.2447-0.00140.5932-0.04040.645-32.1673-24.942735.4011
30.4936-0.5957-0.31980.69130.05071.0181-0.083-0.1936-0.0431-0.27410.11990.11090.1833-0.4951-0.00040.4199-0.1918-0.02460.34420.08550.3408-15.9751-30.24939.6285
40.1783-0.128-0.10190.09430.06860.06320.0609-0.19850.1403-0.64350.0290.33660.1113-0.6064-0.00050.4462-0.0111-0.11810.62860.030.476-25.7898-7.434528.2604
50.39290.2711-0.34750.7750.31130.73020.0052-0.10710.02840.11070.17840.056-0.1285-0.33330.00010.31310.0332-0.00640.2640.06330.3393-12.962-1.891929.4092
60.61240.182-0.13520.71110.26471.3368-0.0435-0.03040.06030.01690.08240.0350.0808-0.3319-0.00010.206-0.0488-0.00150.31010.04540.2932-15.4492-18.8537.2856
70.22770.05690.55880.73820.30541.35690.09830.11010.12050.2259-0.00010.04010.40830.0356-0.00030.3382-0.01080.00740.23640.02210.3249-1.0454-25.450438.076
80.08880.05060.00980.0419-0.00280.02940.5331-0.10070.0768-0.2920.0244-0.1666-0.42930.4728-0.00070.9474-0.1118-0.02880.5493-0.06630.718-11.99218.409517.8001
90.1912-0.0388-0.0750.0363-0.02150.08340.05950.4794-0.19750.73050.64680.3243-0.26350.7971-0.00061.1343-0.15970.14920.7397-0.14990.7898-17.706617.174628.9515
100.10290.016-0.09640.1092-0.0110.0801-0.0666-0.0670.51510.03430.31650.2554-0.2863-0.3843-0.00080.57270.0420.05210.61350.06550.6475-22.0481.468141.5488
110.0009-0.0071-0.00330.05690.04040.04370.12590.48970.41920.56980.54620.2244-0.6510.1811-0.00261.14590.14540.22930.81510.00510.6097-27.51626.212859.3217
124.75672.115.19040.9352.30075.66510.60990.66210.21990.00820.5198-0.48480.5784-0.45490.76280.79230.21740.25970.93380.04050.5957-34.7441-7.168464.3398
130.16350.2194-0.10560.3368-0.2090.21371.4545-0.10970.31430.1038-0.7152-0.4899-0.94780.1350.00650.97980.07030.05251.01440.06160.6461-26.917-7.334560.8521
141.09560.2548-0.97710.90990.6281.71850.65110.05670.2286-0.0737-0.158-0.8436-0.28280.04590.20580.57880.39650.08521.66650.47460.8462-31.39085.718151.2102
150.09840.0485-0.05810.0208-0.0260.02580.0944-0.0921-0.1930.16380.12750.6619-0.3757-0.3804-0.00150.83350.06290.17040.30890.02120.6807-17.08258.167743.8893
160.12420.1615-0.02010.2031-0.03340.0001-0.3544-0.15830.5763-0.26760.39340.0646-0.0235-0.8036-0.00060.71980.0065-0.01410.54790.08360.5916-19.47947.142427.3854
170.06240.02960.04090.0252-0.0110.0599-0.6819-0.1452-0.43990.26540.81570.48420.1201-0.05020.00081.2467-0.08530.02950.74060.19980.6266-14.766217.288415.9855
182.4045-0.76910.80330.8816-0.25571.1852-0.03160.25850.1044-0.2522-0.13960.0926-0.11130.174-0.00010.46260.0217-0.08050.4450.04550.3772-11.4353-45.0152-4.2048
190.19670.1036-0.34160.26380.161.0664-0.22890.2903-0.03260.0504-0.0196-0.34660.7318-0.2149-0.08930.86540.0762-0.09220.6884-0.05980.6702-7.8053-77.8444-0.953
201.8043-0.2624-0.96420.03090.1350.5346-0.3343-1.0699-0.3127-0.4406-0.2665-0.1772-0.50010.7295-0.15430.6532-0.051-0.20220.3385-0.09340.3874-15.0252-59.168618.3763
212.0214-0.35050.99981.35470.01991.77520.0256-0.0696-0.0142-0.1289-0.03780.1673-0.0541-0.3471-0.00010.34580.0165-0.10970.3686-0.03470.418-19.3969-50.23042.2289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 307:315)
2X-RAY DIFFRACTION2(chain A and resid 316:367)
3X-RAY DIFFRACTION3(chain A and resid 368:444)
4X-RAY DIFFRACTION4(chain A and resid 445:466)
5X-RAY DIFFRACTION5(chain A and resid 467:497)
6X-RAY DIFFRACTION6(chain A and resid 498:637)
7X-RAY DIFFRACTION7(chain A and resid 638:700)
8X-RAY DIFFRACTION8(chain B and resid 1:4)
9X-RAY DIFFRACTION9(chain B and resid 5:8)
10X-RAY DIFFRACTION10(chain B and resid 9:15)
11X-RAY DIFFRACTION11(chain B and resid 16:19)
12X-RAY DIFFRACTION12(chain B and resid 20:23)
13X-RAY DIFFRACTION13(chain C and resid 1:5)
14X-RAY DIFFRACTION14(chain C and resid 6:9)
15X-RAY DIFFRACTION15(chain C and resid 10:13)
16X-RAY DIFFRACTION16(chain C and resid 14:18)
17X-RAY DIFFRACTION17(chain C and resid 19:23)
18X-RAY DIFFRACTION18(chain D and resid 304:462)
19X-RAY DIFFRACTION19(chain D and resid 463:479)
20X-RAY DIFFRACTION20(chain D and resid 480:512)
21X-RAY DIFFRACTION21(chain D and resid 513:700)

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