PDB-9q0i: Structure of dsRNA 16mer containing 4'-C-methyladenosine

ID or keywords:

Entry

Database: PDB / ID: 9q0i

Title

Structure of dsRNA 16mer containing 4'-C-methyladenosine

Components

RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

Keywords

RNA / dsRNA / oligonucleotide / 4'-C-methyladenosine / 5-bromouridine

Function / homology

SPERMINE / RNA / RNA (> 10)

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.801 Å

Authors

Jauregui Matos, V. / Fisher, A.J. / Beal, P.A.

Funding support

United States, 1items

Citation

Journal: Chemistry / Year: 2026
Title: Synthesis of 2'-O,4'-C alpha-Dimethyl Ribonucleoside Analogs and Their Effects on RNA and Modulation of ADAR Editing.
Authors: Jauregui-Matos, V. / Brinkman, H.F. / Salvador, P.J. / Jacobs, O. / Cheng, J. / Mozumder, S. / Vu, T. / Fisher, A.J. / Beal, P.A.

History

Deposition	Aug 12, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9q0i.cif.gz	151.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9q0i.ent.gz		Display	PDB format
PDBx/mmJSON format	9q0i.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/q0/9q0i ftp://data.pdbj.org/pub/pdb/validation_reports/q0/9q0i	HTTPS FTP

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Related structure data

Related structure data	9q0jC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #15 - Mar 2001 Transfer RNA similarity (2) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #23 - Nov 2001 DNA similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (2)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)
#23 - Nov 2001
DNA
similarity (1)

Deposited unit

A: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

B: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

C: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

D: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

E: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

F: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

hetero molecules

31.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

B: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

E: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

F: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

hetero molecules

C: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

D: RNA (5'-R(*GP*CP*AP*GP*(AC4)P*CP*UP*(5BU)P*AP*AP*GP*UP*CP*UP*GP*C)-3')

defined by author&software
Evidence: mass spectrometry
31.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.038, 43.038, 127.318
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Auth seq-ID: 1 - 16 / Label seq-ID: 1 - 16

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F

NCS ensembles : (Details: Global NCS restraints between domains: 1 2 3 4 5 6)

#1: RNA chain	RNA (5'-R(GPCPAPGP(AC4)PCPUP(5BU)PAPAPGPUPCPUPGPC)-3') Mass: 5191.002 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-SPM / SPERMINE Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₆N₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.17 Å³/Da / Density % sol: 43.73 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10% MPD, 40 mM Sodium cacodylate trihydrate pH 6.0 12 mM Spermine, 80 mM KCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.91943 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2024
Radiation	Monochromator: Liquid Nireogen Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91943 Å / Relative weight: 1
Reflection	Resolution: 1.8→37.3 Å / Num. obs: 24409 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.029 / R_rim(I) all: 0.094 / Χ²: 0.93 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.8→1.84 Å / Redundancy: 7.3 % / R_merge(I) obs: 1.225 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1436 / CC_1/2: 0.264 / R_pim(I) all: 0.482 / R_rim(I) all: 1.32 / Χ²: 0.78 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
Aimless		data scaling
XDS		data reduction
PDB_EXTRACT		data extraction
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.801→37.3 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.954 / SU B: 9.808 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2459	1252	5.139 %
R_work	0.2122	23113	-
all	0.214	-	-
obs	-	24365	99.73 %

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: 39.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.694 Å²	0.347 Å²	-0 Å²
2-	-	0.694 Å²	-0 Å²
3-	-	-	-2.251 Å²

Refinement step

Cycle: LAST / Resolution: 1.801→37.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	2034	14	101	2149

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.011	2281
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.019	932
X-RAY DIFFRACTION	r_angle_refined_deg	1.803	1.848	3546
X-RAY DIFFRACTION	r_angle_other_deg	0.524	1.686	2274
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.134	5	66
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	474
X-RAY DIFFRACTION	r_chiral_restr_other	0.061	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	1122
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	330
X-RAY DIFFRACTION	r_nbd_refined	0.135	0.2	269
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	1043
X-RAY DIFFRACTION	r_nbtor_refined	0.264	0.2	811
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	592
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.2	86
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.091	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	15
X-RAY DIFFRACTION	r_scbond_it	2.724	3.395	2281
X-RAY DIFFRACTION	r_scbond_other	2.725	3.396	2282
X-RAY DIFFRACTION	r_scangle_it	3.572	6.162	3546
X-RAY DIFFRACTION	r_scangle_other	3.571	6.163	3547
X-RAY DIFFRACTION	r_lrange_it	5.212	47.188	3026
X-RAY DIFFRACTION	r_lrange_other	5.199	47.007	3016

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: loose positional; loose thermal / Weight B_iso : 10 / Weight position: 5

Dom-ID	Auth asym-ID	Rms dev B_iso (Å²)	Rms dev position (Å)
1	A	4.84098	0.65115
2	B	5.17715	0.79592
3	C	5.63511	1.20786
4	D	9.84669	1.18247
5	E	5.5092	0.99819
6	F	7.34829	1.01457

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
1.801-1.847	0.405	77	0.372	1705	0.373	1802	0.886	0.89	98.8901	0.365
1.847-1.898	0.349	94	0.336	1683	0.336	1777	0.91	0.914	100	0.326
1.898-1.953	0.288	78	0.299	1633	0.299	1713	0.94	0.936	99.8832	0.285
1.953-2.013	0.344	84	0.285	1572	0.288	1656	0.924	0.943	100	0.268
2.013-2.078	0.299	98	0.254	1496	0.257	1596	0.937	0.955	99.8747	0.233
2.078-2.151	0.287	84	0.25	1503	0.252	1587	0.946	0.959	100	0.229
2.151-2.232	0.253	68	0.245	1391	0.245	1460	0.959	0.968	99.9315	0.224
2.232-2.323	0.319	78	0.232	1359	0.237	1439	0.95	0.967	99.861	0.209
2.323-2.426	0.277	79	0.242	1323	0.244	1405	0.96	0.966	99.7865	0.224
2.426-2.543	0.282	86	0.238	1272	0.241	1358	0.958	0.967	100	0.225
2.543-2.68	0.301	64	0.232	1173	0.235	1238	0.94	0.967	99.9192	0.227
2.68-2.842	0.291	60	0.243	1146	0.246	1208	0.949	0.963	99.8344	0.242
2.842-3.037	0.206	40	0.214	1066	0.214	1106	0.964	0.972	100	0.227
3.037-3.279	0.251	73	0.212	970	0.215	1055	0.974	0.98	98.8626	0.24
3.279-3.589	0.208	64	0.207	887	0.207	959	0.98	0.982	99.1658	0.234
3.589-4.008	0.241	46	0.183	789	0.185	838	0.961	0.985	99.642	0.211
4.008-4.619	0.142	20	0.164	767	0.164	787	0.981	0.984	100	0.192
4.619-5.635	0.17	22	0.169	629	0.169	653	0.977	0.984	99.6937	0.203
5.635-7.88	0.274	26	0.192	465	0.196	493	0.982	0.984	99.5943	0.225
7.88-37.3	0.151	11	0.172	284	0.171	300	0.99	0.988	98.3333	0.204

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	1.1341	-0.389	0.2961	0.5181	-0.3897	0.2941	-0.0788	-0.1629	-0.0555	-0.0757	0.0951	-0.0137	0.0611	-0.0859	-0.0162	0.0502	-0.0103	-0.0217	0.0413	-0.0018	0.0683	3.1426	29.5459	70.27
2	1.2604	0.2627	-0.5343	0.1045	-0.1115	1.085	0.1586	0.0226	0.0979	0.0399	0.0309	-0.0496	0.0181	-0.1084	-0.1895	0.0282	-0.0044	-0.0143	0.1226	0.0427	0.1621	4.8219	26.5806	92.2035
3	0.817	0.2088	-0.1561	0.8421	0.7139	2.5113	0.1562	0.1692	0.1391	0.0604	0.0991	-0.1738	0.09	-0.2481	-0.2553	0.0347	0.0181	0.0185	0.1615	0.0802	0.124	4.7048	30.0463	88.2579
4	0.731	0.6113	-0.0483	1.6208	0.1573	0.4939	0.0665	-0.006	0.1929	-0.1666	0.1079	0.0191	0.1526	-0.0618	-0.1744	0.1301	-0.0537	-0.0199	0.0648	0.0044	0.1173	-0.2666	28.2326	66.6838
5	1.3353	0.4902	-0.5468	0.1801	-0.2015	0.2302	0.1132	0.0939	0.1785	0.0492	0.0127	0.0695	-0.0638	-0.0527	-0.1259	0.0665	0.0084	0.0406	0.0467	0.0826	0.1575	-16.0766	13.7	55.6971
6	0.2623	0.5828	0.474	1.3276	1.0787	0.8894	0.0523	0.0289	-0.0649	0.071	0.1078	-0.2156	0.0289	0.0474	-0.1601	0.0733	0.054	0.0175	0.0808	-0.0573	0.1742	-20.0525	9.9348	77.3187
7	0.0753	0.4091	0.4877	4.2045	4.5425	4.9672	-0.0668	-0.0009	-0.0302	-0.2727	0.334	-0.2242	-0.3373	0.327	-0.2672	0.0482	0.0078	0.0274	0.0654	-0.0268	0.0716	-17.8031	12.1863	73.6579
8	2.6824	1.4848	-1.6364	0.8646	-0.8165	1.186	-0.0314	0.3478	0.0905	-0.0593	0.1672	0.0032	-0.0289	-0.3098	-0.1359	0.048	0.0101	0.0186	0.1178	0.0943	0.1022	-19.8345	14.9265	52.4414
9	0.3304	0.2167	-0.0745	3.6858	1.1063	0.3965	0.0336	-0.1103	0.0995	0.0302	0.0832	-0.0954	-0.0133	0.0762	-0.1168	0.0787	-0.0621	0.0139	0.0839	-0.0108	0.0977	18.3331	31.6447	32.8389
10	0.928	0.0746	0.3127	0.0472	0.011	0.1136	0.0668	-0.0555	-0.0164	-0.016	-0.0098	0.0793	0.0313	-0.0061	-0.0569	0.0469	-0.0289	-0.0335	0.0851	-0.0124	0.1744	17.7096	37.2921	55.0374
11	2.5602	-0.4284	-1.5437	0.7607	0.0472	1.2635	0.2252	-0.0874	-0.3344	-0.1376	0.0005	0.482	-0.1513	0.3003	-0.2257	0.0511	-0.0048	-0.1056	0.2887	-0.1444	0.4598	17.8289	33.6174	51.3234
12	0.9638	0.7691	-0.0509	4.4221	-1.5087	0.5732	-0.0555	-0.1931	-0.2759	-0.3921	0.0228	-0.374	0.1215	-0.0554	0.0326	0.1447	-0.0741	0.0924	0.0864	0.0052	0.1329	21.8841	33.5597	29.5313

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 8
2	X-RAY DIFFRACTION	2	ALL	A	9 - 16
3	X-RAY DIFFRACTION	3	ALL	B	1 - 8
4	X-RAY DIFFRACTION	4	ALL	B	9 - 16
5	X-RAY DIFFRACTION	5	ALL	C	1 - 8
6	X-RAY DIFFRACTION	6	ALL	C	9 - 16
7	X-RAY DIFFRACTION	7	ALL	D	1 - 8
8	X-RAY DIFFRACTION	8	ALL	D	9 - 16
9	X-RAY DIFFRACTION	9	ALL	E	1 - 8
10	X-RAY DIFFRACTION	10	ALL	E	9 - 16
11	X-RAY DIFFRACTION	11	ALL	F	1 - 8
12	X-RAY DIFFRACTION	12	ALL	F	9 - 16

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