PDB-9q0j: Structure of dsRNA 16mer containing 4'-C-methyluridine

ID or keywords:

Entry

Database: PDB / ID: 9q0j

Title

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

Components

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

Keywords

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

Function / homology

RNA / RNA (> 10)

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 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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PDBx/mmCIF format	9q0j.cif.gz	80.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9q0j.ent.gz		Display	PDB format
PDBx/mmJSON format	9q0j.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/9q0j ftp://data.pdbj.org/pub/pdb/validation_reports/q0/9q0j	HTTPS FTP

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Related structure data

Related structure data	9q0iC 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) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA 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)

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)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
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)

Deposited unit

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

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

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

15.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

defined by author&software
Evidence: mass spectrometry
10.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

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

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

defined by author&software
10.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.081, 42.928, 49.294
Angle α, β, γ (deg.)	90.000, 120.019, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

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	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	A	A
2	1	1	B	B
3	2	2	A	A
4	2	2	C	C
5	3	3	B	B
6	3	3	C	C

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: RNA chain	RNA (5'-R(GPCPAPGPAPCPUP(5BU)PAPAPGP(UCD)PCPUPGPC)-3') Mass: 5191.001 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.22 Å³/Da / Density % sol: 43.55 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop 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: 0.92002 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: 0.92002 Å / Relative weight: 1
Reflection	Resolution: 2→33 Å / Num. obs: 9056 / % possible obs: 98.5 % / Redundancy: 3.3 % / CC_1/2: 0.994 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.049 / R_rim(I) all: 0.09 / Net I/σ(I): 5.3
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.622 / Num. unique obs: 687 / CC_1/2: 0.691 / R_pim(I) all: 0.398 / R_rim(I) all: 0.741 / % possible all: 98.8

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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: 2→32.143 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.97 / SU B: 23.726 / SU ML: 0.251 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2499	492	5.433 %
R_work	0.2248	8563	-
all	0.226	-	-
obs	-	9055	98.381 %

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: 53.496 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.303 Å²	-0 Å²	-0.06 Å²
2-	-	0.108 Å²	-0 Å²
3-	-	-	-0.805 Å²

Refinement step

Cycle: LAST / Resolution: 2→32.143 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	1017	0	4	1021

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.011	1134
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.019	456
X-RAY DIFFRACTION	r_angle_refined_deg	1.691	1.847	1767
X-RAY DIFFRACTION	r_angle_other_deg	0.49	1.683	1110
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.404	5	36
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	246
X-RAY DIFFRACTION	r_gen_planes_refined	0.029	0.02	567
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	168
X-RAY DIFFRACTION	r_nbd_refined	0.147	0.2	117
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	518
X-RAY DIFFRACTION	r_nbtor_refined	0.261	0.2	452
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.098	0.2	304
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.117	0.2	24
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	26
X-RAY DIFFRACTION	r_scbond_it	3.461	1.202	1134
X-RAY DIFFRACTION	r_scbond_other	3.459	1.201	1135
X-RAY DIFFRACTION	r_scangle_it	4.982	2.204	1767
X-RAY DIFFRACTION	r_scangle_other	4.981	2.203	1768
X-RAY DIFFRACTION	r_lrange_it	5.756	13.583	1529
X-RAY DIFFRACTION	r_lrange_other	5.755	13.578	1530
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.014	0.05	1557
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.014	0.05	1553
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.014	0.05	1551

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	0.01385	0.05012
1	2	B	X-RAY DIFFRACTION	Local ncs	0.01385	0.05012
2	3	A	X-RAY DIFFRACTION	Local ncs	0.01422	0.05012
2	4	C	X-RAY DIFFRACTION	Local ncs	0.01422	0.05012
3	5	B	X-RAY DIFFRACTION	Local ncs	0.01419	0.05012
3	6	C	X-RAY DIFFRACTION	Local ncs	0.01419	0.05012

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
2-2.052	0.476	35	0.437	646	0.439	691	0.84	0.869	98.5528	0.41
2.052-2.108	0.33	35	0.434	617	0.428	662	0.908	0.833	98.4894	0.417
2.108-2.169	0.394	30	0.414	575	0.413	611	0.883	0.87	99.018	0.399
2.169-2.235	0.517	29	0.373	592	0.378	632	0.797	0.9	98.2595	0.352
2.235-2.308	0.472	30	0.379	532	0.385	577	0.781	0.883	97.4004	0.368
2.308-2.389	0.42	30	0.361	533	0.364	590	0.88	0.923	95.4237	0.356
2.389-2.478	0.28	21	0.342	543	0.34	570	0.94	0.946	98.9474	0.331
2.478-2.579	0.317	26	0.318	511	0.318	540	0.961	0.952	99.4444	0.306
2.579-2.693	0.497	25	0.311	503	0.319	532	0.847	0.944	99.2481	0.309
2.693-2.823	0.25	34	0.309	444	0.305	480	0.951	0.95	99.5833	0.294
2.823-2.974	0.378	32	0.278	439	0.283	478	0.932	0.973	98.5356	0.301
2.974-3.153	0.222	23	0.215	410	0.216	440	0.988	0.987	98.4091	0.252
3.153-3.369	0.217	28	0.225	382	0.224	424	0.987	0.989	96.6981	0.259
3.369-3.635	0.213	22	0.221	371	0.22	400	0.976	0.981	98.25	0.257
3.635-3.977	0.194	19	0.176	346	0.177	368	0.994	0.992	99.1848	0.21
3.977-4.438	0.136	23	0.153	298	0.151	324	0.992	0.988	99.0741	0.187
4.438-5.108	0.185	23	0.144	273	0.147	298	0.984	0.989	99.3289	0.199
5.108-6.217	0.308	14	0.154	245	0.16	262	0.965	0.989	98.855	0.198
6.217-8.633	0.374	8	0.178	184	0.183	197	0.928	0.987	97.4619	0.224
8.633-32.143	0.361	5	0.117	119	0.124	125	0.935	0.994	99.2	0.157

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	1.7689	-0.2299	-0.469	0.1692	-0.2309	0.7685	0.1652	0.2735	0.1473	-0.0882	0.2082	0.126	0.17	-0.4513	-0.3734	0.5864	-0.0569	0.0026	0.685	0.0652	0.3034	62.9066	20.9324	30.4692
2	3.3949	-1.8518	0.731	3.2955	0.3831	0.4597	0.1899	-0.1917	-0.0056	0.1656	0.0523	-0.0569	0.1801	0.0004	-0.2422	0.5355	-0.0047	-0.0327	0.6188	-0.0537	0.2695	58.4587	17.6473	8.7115
3	0.4521	-0.4076	-0.4176	0.3807	0.3743	0.3864	0.1041	-0.1924	0.2201	-0.0647	0.1594	-0.1679	-0.1704	0.1838	-0.2635	0.8399	0.0379	0.0492	0.738	0.0668	0.376	45.3083	33.2785	12.2141
4	3.6598	0.0416	0.0531	0.769	0.5693	0.4716	0.0579	0.0535	-0.0136	-0.1428	0.1548	-0.075	-0.0453	0.1468	-0.2127	0.5636	0.0037	-0.0287	0.5917	-0.037	0.2638	45.9373	38.7743	33.9661
5	0.886	-0.8138	0.4728	1.4204	-0.2044	0.3412	0.3946	0.1299	-0.3123	-0.2892	0.0243	0.0576	0.3064	0.1938	-0.4189	0.651	0.0503	-0.1099	0.7344	-0.0672	0.314	44.1727	35.2825	30.4495
6	3.3169	1.3629	-0.1248	4.1518	1.2068	1.0703	0.2113	-0.2663	-0.2803	-0.0027	0.2966	-0.0423	-0.1699	0.0603	-0.5079	0.6116	0.0151	0.0647	0.6843	0.0518	0.3683	49.2077	33.0394	8.7164

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

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