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- PDB-5hp2: Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA ... -

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Basic information

Entry
Database: PDB / ID: 5hp2
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA sequence derived from S. cerevisiae BDF2 gene with AU basepair at reaction site
Components
  • Double-stranded RNA-specific editase 1
  • RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*UP*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 / double-stranded RNA adenosine deaminase activity ...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 / 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 / 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 / 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: 2.983 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*UP*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
Polymers104,7274
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*UP*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
Polymers104,7274
Non-polymers1,4514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area9670 Å2
ΔGint-155 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.320, 106.680, 120.490
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*UP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3')


Mass: 7490.546 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% PEG10000

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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: 2.98→80.4 Å / Num. obs: 21442 / % possible obs: 97.3 % / Redundancy: 4.787 % / CC1/2: 0.991 / Rmerge(I) obs: 0.144 / Net I/σ(I): 10
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 4.562 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.88 / % possible all: 90

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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: 2.983→38.526 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.2467 1084 5.07 %
Rwork0.1667 --
obs0.1708 21376 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.983→38.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6168 973 74 1 7216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097462
X-RAY DIFFRACTIONf_angle_d1.35910329
X-RAY DIFFRACTIONf_dihedral_angle_d15.4662928
X-RAY DIFFRACTIONf_chiral_restr0.0541195
X-RAY DIFFRACTIONf_plane_restr0.0071146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9834-3.11910.41651190.30792400X-RAY DIFFRACTION93
3.1191-3.28340.32321340.22852533X-RAY DIFFRACTION99
3.2834-3.4890.31681270.2042467X-RAY DIFFRACTION96
3.489-3.75820.2591250.1832558X-RAY DIFFRACTION99
3.7582-4.1360.25651550.14712539X-RAY DIFFRACTION99
4.136-4.73360.2211360.13512524X-RAY DIFFRACTION97
4.7336-5.96030.21581350.13912618X-RAY DIFFRACTION99
5.9603-38.52880.19451530.14962653X-RAY DIFFRACTION96
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)
10.28510.04430.22660.26880.02540.1538-0.06690.10630.1697-0.2726-0.28290.6336-0.0658-0.13250.00030.448-0.0380.02140.6689-0.01190.6163-31.6742-21.931632.185
20.3405-0.0479-0.41940.464-0.06890.2156-0.0316-0.219-0.0243-0.08550.0287-0.03270.0465-0.4047-0.00590.3307-0.1348-0.02030.35770.08740.3351-18.9179-27.151741.0945
30.3268-0.07420.51660.53020.33150.7714-0.0343-0.0586-0.123-0.0550.06270.29070.1582-0.25650.0390.4146-0.1110.03730.36090.02750.3933-19.8675-24.324329.4659
40.0359-0.00090.01690.17090.07470.12290.1899-0.1618-0.1964-0.2717-0.0270.2285-0.23070.0167-0.07520.67640.1447-0.15751.05980.34190.9699-26.8113-1.140216.7311
50.09810.0393-0.02150.10620.16570.13650.0893-0.13750.27830.17630.1428-0.03210.52720.3320.01230.32550.03510.02780.32310.03850.3006-11.0388-1.89431.2998
6-0.01870.1561-0.09870.11360.14950.9139-0.0847-0.0690.0110.06250.05840.03580.0834-0.1779-00.2736-0.02950.00780.33980.01290.3484-15.501-18.687437.1331
70.03710.15150.40250.17790.26930.8497-0.04240.20960.0350.14660.0493-0.08190.1751-0.07840.00550.2401-0.03170.03830.25050.01730.3357-0.9718-25.137437.9916
80.00040.00470.0145-0.00190.01740.01470.128-0.33180.032-0.34650.2740.3262-0.02540.03330.00010.8365-0.1489-0.07780.5609-0.15790.6412-12.1268.843517.6914
90.10670.04220.05730.00690.04670.21520.65810.0371-0.00870.20850.72250.1825-0.42010.79140.01051.1973-0.13130.23170.5334-0.04370.7968-19.709615.970629.7148
100.6518-0.42440.8831.0342-1.06281.54860.4205-0.28950.1767-0.06180.14640.5661-0.0181-1.02970.34630.47480.03310.04490.31770.06220.3675-22.174-0.375740.8936
110.04180.03060.0040.026-0.0013-0.0013-0.0290.3610.00370.4677-0.0053-0.0613-0.01890.017800.62690.07640.10110.76530.04360.5084-23.97585.538457.3102
12-0.0054-0.01430.00030.0019-0.00140.0470.4571-0.3780.4796-0.0526-0.1230.3901-0.20810.0598-0.0010.71940.02110.16850.6376-0.04660.7998-34.6131-5.590663.7131
130.00270.01010.00630.00270.00490.00230.5181-0.027-0.0840.0914-0.3043-0.0948-0.56210.03910.00070.78740.08850.08060.59040.09610.6107-27.0266-7.878360.5935
140.0090.01080.01490.009-0.00610.01020.2390.1890.38240.0844-0.0431-0.17880.51650.03730.00040.62830.29860.15291.03850.36460.7561-31.3925.468751.1315
150.14960.04620.1730.0120.05770.21880.092-0.14620.2113-0.16650.10460.68030.1625-0.3083-0.0020.8705-0.03220.1643-0.49810.08930.5871-17.30148.289943.9125
160.06520.0463-0.06520.0136-0.04480.044-0.1676-0.22480.0572-0.256-0.0180.19920.292-0.1306-00.5840.0142-0.050.40860.18010.5506-19.71127.288227.1764
170.0139-0.00580.0043-0.01050.00720.04870.00080.19140.02180.40330.54630.4938-0.2540.1753-0.00081.26570.01410.17750.52940.0450.6842-14.915217.596515.9223
180.7032-0.45150.02950.0221-0.1410.2815-0.14680.08650.0996-0.13090.04030.0610.02930.049800.5279-0.0191-0.03410.5301-0.00150.4388-7.4814-44.6132-1.8197
190.4392-0.53360.06811.63450.34880.15460.23040.5861-0.1115-0.5182-0.39540.2792-0.05390.0559-1.29280.50290.0929-0.06880.50420.02920.4015-17.0255-45.7259-8.3821
202.0023-4.98946.10038.51535.73131.99812.06280.062-3.1661.55250.10290.78863.5031-0.7732-2.22391.00190.2139-0.58260.68010.32951.3305-7.1954-80.4255-5.0655
215.62650.80521.52022.1854-1.88435.72520.3676-0.1123-0.7665-0.2243-0.4067-0.02341.24660.6875-0.3750.59790.1095-0.04110.24050.01910.4245-9.4724-64.621310.587
220.6704-0.3616-0.12471.02730.42861.21180.11440.011-0.1085-0.1234-0.0350.0778-0.0206-0.1066-00.3430.0224-0.10770.3008-0.01870.366-16.4947-49.47862.7238
230.04010.01840.01040.01760.0183-0.0047-0.04860.21680.04240.1202-0.13560.69590.1354-0.2822-0.00090.66380.0479-0.08151.2182-0.1830.9025-35.2015-44.98748.8834
240.12680.03460.07980.1316-0.16320.1034-0.1187-0.3501-0.4592-0.35530.0470.5442-0.0151-0.5392-0.00030.38620.0701-0.08480.568-0.06130.6221-26.9712-55.57777.1765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 305:349)
2X-RAY DIFFRACTION2(chain A and resid 350:422)
3X-RAY DIFFRACTION3(chain A and resid 423:464)
4X-RAY DIFFRACTION4(chain A and resid 465:470)
5X-RAY DIFFRACTION5(chain A and resid 471:498)
6X-RAY DIFFRACTION6(chain A and resid 499:637)
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 5:9)
10X-RAY DIFFRACTION10(chain B and resid 10:14)
11X-RAY DIFFRACTION11(chain B and resid 15:18)
12X-RAY DIFFRACTION12(chain B and resid 19:23)
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 304:406)
19X-RAY DIFFRACTION19(chain D and resid 407:464)
20X-RAY DIFFRACTION20(chain D and resid 465:471)
21X-RAY DIFFRACTION21(chain D and resid 472:494)
22X-RAY DIFFRACTION22(chain D and resid 495:652)
23X-RAY DIFFRACTION23(chain D and resid 653:659)
24X-RAY DIFFRACTION24(chain D and resid 660:700)

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