PDB-9dp5: Crystal Structure of Hydra Adenosine Deaminase Acting on RNA (ADA...

ID or keywords:

Entry

Database: PDB / ID: 9dp5

Title

Crystal Structure of Hydra Adenosine Deaminase Acting on RNA (ADAR) Deaminase Domain

Components

Double-stranded RNA-specific editase Adar-like

Keywords

RNA BINDING PROTEIN / RNA Editing / Deaminase / Adenosine / Inosine / ADAR

Function / homology

Function and homology information

tRNA-specific adenosine deaminase activity / adenosine to inosine editing / double-stranded RNA adenosine deaminase activity / adenosine deaminase activity / RNA processing / double-stranded RNA binding / nucleolus / cytoplasm
Similarity search - Function

Biological species

Hydra vulgaris (swiftwater hydra)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.998 Å

Authors

Fisher, A.J. / Wilcox, X.E.

Funding support

United States, 1items

Citation

Journal: Arch.Biochem.Biophys. / Year: 2025
Title: Phylogenetic and structural analysis of Hydra ADAR.
Authors: Wilcox, X.E. / Zhang, H. / Mah, J.L. / Cazet, J.F. / Mozumder, S. / Venkatesh, S. / Juliano, C.E. / Beal, P.A. / Fisher, A.J.

History

Deposition	Sep 20, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dp5.cif.gz	377 KB	Display	PDBx/mmCIF format
PDB format	pdb9dp5.ent.gz	238.8 KB	Display	PDB format
PDBx/mmJSON format	9dp5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dp/9dp5 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/9dp5	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #225 - Sep 2018 Phytase similarity (1) #105 - Sep 2008 Ribonuclease A similarity (3) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1) #88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: Double-stranded RNA-specific editase Adar-like

B: Double-stranded RNA-specific editase Adar-like

hetero molecules

85.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Double-stranded RNA-specific editase Adar-like

hetero molecules

defined by author
Evidence: Based on crystal packing and low buried surface area and water-mediated interactions.
42.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Double-stranded RNA-specific editase Adar-like

hetero molecules

defined by author
42.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.400, 49.440, 83.040
Angle α, β, γ (deg.)	83.109, 80.171, 71.060
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 497 - 863 / Label seq-ID: 6 - 372

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	Double-stranded RNA-specific editase Adar-like / Double-stranded RNA-specific editase B2 Mass: 41599.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Gene: ADARB2, LOC100198026 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: T2M593

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Non-polymers , 5 types, 99 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 45.73 % / Description: rod-shaped crystal
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5, 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2021
Radiation	Monochromator: Liquid nitrogen-cooled double crystal, Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.998→65 Å / Num. obs: 47063 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.52 % / B_iso Wilson estimate: 34.79 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.094 / R_rim(I) all: 0.111 / Net I/σ(I): 7.79
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 3.54 % / R_merge(I) obs: 1.123 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 3516 / CC_1/2: 0.737 / R_rim(I) all: 1.323 / % possible all: 95.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.998→39.376 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.942 / SU B: 12.43 / SU ML: 0.168 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2429	2542	5.401 %
R_work	0.2111	44521	-
all	0.213	-	-
obs	-	47063	94.96 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 53.135 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.732 Å²	1.705 Å²	0.885 Å²
2-	-	0.447 Å²	1.471 Å²
3-	-	-	0.216 Å²

Refinement step

Cycle: LAST / Resolution: 1.998→39.376 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5481	0	99	88	5668

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	5704
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	5468
X-RAY DIFFRACTION	r_angle_refined_deg	1.672	1.829	7699
X-RAY DIFFRACTION	r_angle_other_deg	0.591	1.763	12606
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.762	5	696
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.577	5	28
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.562	10	1005
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.514	10	241
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	868
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6487
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1297
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1182
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	5078
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2756
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	3058
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	179
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.144	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.22	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.113	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.867	2.612	2793
X-RAY DIFFRACTION	r_mcbond_other	2.865	2.612	2793
X-RAY DIFFRACTION	r_mcangle_it	5.027	4.665	3480
X-RAY DIFFRACTION	r_mcangle_other	5.027	4.667	3481
X-RAY DIFFRACTION	r_scbond_it	2.845	2.931	2911
X-RAY DIFFRACTION	r_scbond_other	2.845	2.932	2912
X-RAY DIFFRACTION	r_scangle_it	4.624	5.245	4217
X-RAY DIFFRACTION	r_scangle_other	4.623	5.246	4218
X-RAY DIFFRACTION	r_lrange_it	8.638	27.332	6276
X-RAY DIFFRACTION	r_lrange_other	8.639	27.327	6272
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.135	0.05	10561

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.13506	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.13506	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.998-2.049	0.321	173	0.309	3161	0.31	3671	0.917	0.922	90.8199	0.296
2.049-2.105	0.308	178	0.296	3257	0.297	3529	0.928	0.93	97.3364	0.28
2.105-2.166	0.3	199	0.274	3180	0.275	3492	0.932	0.94	96.764	0.248
2.166-2.233	0.284	166	0.265	3082	0.265	3388	0.93	0.945	95.8678	0.237
2.233-2.306	0.246	165	0.247	2801	0.247	3254	0.959	0.955	91.1494	0.216
2.306-2.386	0.264	160	0.221	2853	0.223	3166	0.949	0.965	95.1674	0.192
2.386-2.476	0.219	170	0.2	2832	0.201	3087	0.97	0.973	97.2465	0.173
2.476-2.577	0.264	149	0.202	2642	0.205	2892	0.96	0.974	96.5076	0.176
2.577-2.691	0.255	153	0.2	2543	0.203	2787	0.957	0.975	96.7348	0.178
2.691-2.821	0.278	120	0.203	2348	0.206	2685	0.958	0.974	91.9181	0.184
2.821-2.973	0.246	129	0.194	2355	0.196	2584	0.96	0.978	96.13	0.179
2.973-3.152	0.239	134	0.2	2177	0.202	2400	0.967	0.977	96.2917	0.192
3.152-3.368	0.225	114	0.207	2089	0.208	2292	0.97	0.976	96.1169	0.202
3.368-3.636	0.255	105	0.21	1881	0.212	2127	0.959	0.977	93.3709	0.214
3.636-3.98	0.234	107	0.21	1700	0.212	1937	0.973	0.977	93.2886	0.217
3.98-4.444	0.195	94	0.18	1636	0.181	1782	0.976	0.981	97.0819	0.199
4.444-5.12	0.2	79	0.169	1399	0.171	1538	0.977	0.983	96.0988	0.197
5.12-6.245	0.238	63	0.219	1165	0.22	1338	0.969	0.975	91.7788	0.252
6.245-8.722	0.265	53	0.214	911	0.217	1010	0.959	0.976	95.4455	0.265
8.722-39.376	0.278	31	0.247	510	0.249	596	0.951	0.968	90.7718	0.32

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.4716	-1.1931	0.7008	2.3493	-1.3059	2.5731	-0.0628	-0.0115	0.1588	0.1622	-0.0245	-0.2233	-0.1442	0.2101	0.0873	0.2033	-0.0363	-0.0148	0.1785	-0.002	0.1789	10.3416	22.5539	89.5245
2	0.9049	-1.2778	-0.2774	3.0509	-0.0771	2.4701	-0.1072	0.0015	-0.1085	0.1424	0.0389	0.1206	0.0367	-0.0303	0.0683	0.2003	-0.0175	0.0217	0.2573	0.0456	0.2056	3.6268	13.7854	90.0962
3	1.9304	-1.7569	0.4623	2.2909	-0.7312	2.5196	-0.4929	-0.4275	-0.0134	0.727	0.3854	-0.0239	-0.1727	0.0089	0.1075	0.3365	0.1126	0.022	0.2452	0.0643	0.0369	8.4915	12.4214	104.2251
4	1.624	-1.0919	-1.1689	1.7563	-0.0864	2.2904	0.1305	0.2724	-0.1271	-0.0736	-0.172	0.1716	-0.0688	-0.1972	0.0416	0.2017	0.0298	-0.0062	0.3215	0.0245	0.1914	18.9613	-2.2293	60.0221
5	2.0922	-1.5034	-0.1923	1.722	-0.4406	2.6641	-0.0124	0.0912	0.0565	0.0209	-0.085	-0.2223	0.0031	0.1704	0.0975	0.2388	-0.0306	0.02	0.2501	0.038	0.2239	32.6054	-6.0402	65.5964
6	1.5116	-1.0755	-0.2212	2.4055	0.4702	2.1663	0.2151	0.3922	-0.1257	-0.448	-0.3133	0.0183	0.0691	-0.1287	0.0982	0.2742	0.0834	0.0379	0.2882	0.0142	0.0427	27.5972	-9.6069	50.1367

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	497 - 582
2	X-RAY DIFFRACTION	2	ALL	A	583 - 765
3	X-RAY DIFFRACTION	3	ALL	A	766 - 863

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