PDB-9o5b: RNase A in complex with N1-Methylpseudouridine Vanadate and decav...

ID or keywords:

Entry

Database: PDB / ID: 9o5b

Title

RNase A in complex with N1-Methylpseudouridine Vanadate and decavanadates

Components

Ribonuclease pancreatic

Keywords

HYDROLASE / Ribonuclease / RNA / N1-Methylpseudouridine Vanadate / decavanadate

Function / homology

Function and homology information

pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.71 Å

Authors

Gutierrez, C.S. / Lim, D.C. / Silkenath, B. / Kojasoy, V. / Raines, R.T.

Funding support

United States, 1items

Citation

Journal: Rna / Year: 2025
Title: Pseudouridine residues as substrates for serum ribonucleases.
Authors: Gutierrez, C.S. / Silkenath, B. / Kojasoy, V. / Pich, J.A. / Lim, D.C. / Raines, R.T.

History

Deposition	Apr 9, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 29, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9o5b.cif.gz	159.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9o5b_validation.pdf.gz	3.6 MB	Display	wwPDB validaton report
Full document	9o5b_full_validation.pdf.gz	3.7 MB	Display
Data in XML	9o5b_validation.xml.gz	16.8 KB	Display
Data in CIF	9o5b_validation.cif.gz	22.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o5/9o5b ftp://data.pdbj.org/pub/pdb/validation_reports/o5/9o5b	HTTPS FTP

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Related structure data

Related structure data	9ncsC 9o4vC C: citing same article (ref.)
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	#105 - Sep 2008 Ribonuclease A similarity (9) #143 - Nov 2011 Toll-like Receptors similarity (9)

Deposited unit

A: Ribonuclease pancreatic

B: Ribonuclease pancreatic

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	100.310, 32.830, 72.670
Angle α, β, γ (deg.)	90.00, 90.55, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-360- HOH
2	1	B-306- HOH

#1: Protein	Ribonuclease pancreatic / RNase 1 / RNase A Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Pancreas / Plasmid details: Millipore Sigma R6513 / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical	ChemComp-8IZ / 5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione Mass: 258.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-DVT / DECAVANADATE Mass: 957.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O₂₈V₁₀
#4: Chemical	ChemComp-VVO / oxovanadium(2+) Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.74 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystallization: 20mM Sodium Citrate pH 5.5, 25% PEG 4000 seeded with crystals grown in 20mM Sodium Citrate pH 5.5, 20% PEG 4000 Ligand soaking: 16.7mM Imidazole pH 5.5, 30% PEG 4000, 5% ...Details: Crystallization: 20mM Sodium Citrate pH 5.5, 25% PEG 4000 seeded with crystals grown in 20mM Sodium Citrate pH 5.5, 20% PEG 4000 Ligand soaking: 16.7mM Imidazole pH 5.5, 30% PEG 4000, 5% glycerol, 5mM N1-methylpseudouridine Vanadate

Crystal

Density Matthews: 2.19 Å³/Da / Density % sol: 43.74 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystallization: 20mM Sodium Citrate pH 5.5, 25% PEG 4000 seeded with crystals grown in 20mM Sodium Citrate pH 5.5, 20% PEG 4000 Ligand soaking: 16.7mM Imidazole pH 5.5, 30% PEG 4000, 5% ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 26, 2024 / Details: Varimax HF

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.71→25.08 Å / Num. obs: 22880 / % possible obs: 25.4 % / Redundancy: 4.3 % / CC_1/2: 0.993 / R_merge(I) obs: 0.04 / R_rim(I) all: 0.057 / Net I/σ(I): 8.8

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.71-1.81	0.13	347	0.947	0.184	1
1.81-1.93	0.111	786	0.956	0.157	1
1.93-2.09	0.058	1113	0.987	0.083	1
2.09-2.29	0.039	1041	0.991	0.056	1
2.29-2.55	0.034	943	0.994	0.049	1
2.55-2.95	0.05	833	0.986	0.071	1
2.95-3.61	0.045	736	0.987	0.063	1
3.61-5.08	0.029	537	0.995	0.041	1
5.08-25.08	0.033	316	0.993	0.047	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.71→25.08 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2191	3553	8.83 %
R_work	0.1819	-	-
obs	0.1851	40231	80 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.71→25.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1857	0	172	231	2260

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2272
X-RAY DIFFRACTION	f_angle_d	1.145	3818
X-RAY DIFFRACTION	f_dihedral_angle_d	12.759	791
X-RAY DIFFRACTION	f_chiral_restr	0.061	286
X-RAY DIFFRACTION	f_plane_restr	0.019	336

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.71-1.73	0.3657	22	0.3503	310	X-RAY DIFFRACTION	16
1.73-1.76	0.3834	69	0.3721	654	X-RAY DIFFRACTION	36
1.76-1.78	0.3692	65	0.3424	808	X-RAY DIFFRACTION	44
1.78-1.81	0.3467	98	0.3229	980	X-RAY DIFFRACTION	52
1.81-1.84	0.3669	109	0.3128	1101	X-RAY DIFFRACTION	61
1.84-1.87	0.4457	112	0.3452	1274	X-RAY DIFFRACTION	70
1.87-1.91	0.4005	140	0.2786	1381	X-RAY DIFFRACTION	75
1.91-1.94	0.3154	150	0.2472	1544	X-RAY DIFFRACTION	83
1.94-1.98	0.2357	153	0.2259	1517	X-RAY DIFFRACTION	86
1.98-2.03	0.2942	157	0.2104	1617	X-RAY DIFFRACTION	86
2.03-2.07	0.2929	155	0.1938	1563	X-RAY DIFFRACTION	86
2.07-2.12	0.2374	157	0.1907	1570	X-RAY DIFFRACTION	86
2.12-2.18	0.2427	164	0.1725	1642	X-RAY DIFFRACTION	88
2.18-2.25	0.2075	142	0.1712	1560	X-RAY DIFFRACTION	88
2.25-2.32	0.2484	153	0.1684	1666	X-RAY DIFFRACTION	89
2.32-2.4	0.1899	166	0.1547	1699	X-RAY DIFFRACTION	90
2.4-2.5	0.185	156	0.1561	1647	X-RAY DIFFRACTION	91
2.5-2.61	0.1746	163	0.1599	1680	X-RAY DIFFRACTION	92
2.61-2.75	0.1913	176	0.1772	1735	X-RAY DIFFRACTION	94
2.75-2.92	0.2336	174	0.1721	1759	X-RAY DIFFRACTION	96
2.92-3.14	0.1836	156	0.1764	1751	X-RAY DIFFRACTION	96
3.15-3.46	0.1999	172	0.1666	1805	X-RAY DIFFRACTION	98
3.46-3.96	0.1994	170	0.1512	1799	X-RAY DIFFRACTION	99
3.96-4.98	0.154	188	0.1439	1815	X-RAY DIFFRACTION	99
4.98-25.08	0.2354	186	0.2177	1801	X-RAY DIFFRACTION	99

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	3.4888	-1.6967	2.4098	4.7655	-1.8753	5.3786	0.0968	0.273	-0.1002	-0.3397	0.0388	0.2608	0.3762	-0.0135	-0.0713	0.1633	-0.0142	-0.011	0.1659	-0.0196	0.1121	16.1844	-3.7442	3.5069
2	2.0883	0.7387	0.8689	0.9221	0.4829	3.3558	-0.0884	0.1416	0.1295	-0.0696	0.0476	0.1221	-0.0616	0.0644	0.0632	0.0933	0.0038	0.0054	0.0844	-0.0051	0.1183	19.6228	1.8631	13.3444
3	7.2759	-3.8073	-0.0323	7.7614	0.2308	7.7481	0.1445	0.2709	0.2916	-0.1314	-0.1388	-0.0826	-0.3363	-0.0203	-0.033	0.0985	-0.0038	0.0152	0.1464	-0.0059	0.1157	33.5416	7.1576	31.2129
4	4.1534	-0.5262	-2.5534	3.6147	0.9153	4.0478	-0.0979	0.9762	-0.5475	-0.444	-0.0786	0.0183	0.7386	-0.1455	0.1949	0.2881	0.0437	0.0138	0.3968	-0.107	0.203	38.6185	-3.4463	21.0524
5	8.4681	1.3148	-1.5365	3.4716	-1.5599	3.589	0.0678	0.9093	0.8398	-0.2606	-0.0563	-0.244	-0.3077	0.1689	-0.039	0.2303	0.0604	0.0069	0.3229	0.0446	0.2431	41.7153	7.9425	21.4219
6	2.8537	0.2951	-0.6595	2.1815	-1.1367	3.4344	0.0679	0.2562	-0.2686	-0.2675	-0.005	-0.0259	0.3356	0.0103	-0.0311	0.1493	0.0169	-0.0046	0.1468	-0.0218	0.1737	34.9496	-4.0215	35.2414
7	7.9479	3.1862	0.3241	7.2749	0.1324	4.7074	-0.1633	-0.1406	0.3779	0.2889	-0.1144	-0.5421	-0.4687	0.4648	0.0479	0.1512	-0.0373	-0.0365	0.1481	0.0058	0.1894	42.1756	3.5495	47.1191
8	2.3018	0.6627	-1.3322	1.1452	-0.9735	3.5551	0.0405	0.1599	-0.2124	-0.1369	-0.1739	-0.0865	0.1674	0.1685	0.1504	0.1151	0.0509	-0.0044	0.1485	-0.0131	0.1624	42.1821	-5.045	36.0425
9	1.6741	-0.5467	-0.4513	3.5883	-1.6927	2.9972	0.0878	0.8518	0.2783	-0.5233	-0.054	-0.3204	-0.1902	0.3591	0.0829	0.3097	0.0841	0.0714	0.6475	0.0609	0.3314	50.2219	5.4446	15.1227
10	1.3444	0.569	-1.4582	1.3024	-1.0505	4.1698	-0.0049	0.415	-0.2973	-0.2649	-0.1816	-0.1475	0.4488	0.3338	0.26	0.183	0.0507	0.0165	0.2637	-0.027	0.1729	44.246	-5.9083	31.8228
11	5.4325	-0.0993	-1.7371	1.7165	-0.3165	4.0844	0.0514	-0.0322	0.0841	-0.0341	-0.0725	-0.0381	-0.2343	0.0769	-0.069	0.1575	-0.033	-0.0036	0.0981	-0.0127	0.153	36.0001	3.3637	40.6405

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 124 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 12 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 13 through 32 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 33 through 42 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 43 through 59 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 71 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 72 through 86 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 87 through 96 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 97 through 109 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 110 through 124 )

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