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- PDB-9o4v: RNase A in complex with Pseudouridine Vanadate and decavanadates -

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Basic information

Entry
Database: PDB / ID: 9o4v
TitleRNase A in complex with Pseudouridine Vanadate and decavanadates
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease / pseudouridine / pseudouridine 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
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Pancreatic ribonuclease
Similarity search - Domain/homology
DECAVANADATE / Chem-FJF / oxovanadium(2+) / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGutierrez, C.S. / Lim, D.C. / Silkenath, B. / Kojasoy, V. / Raines, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA073808 United States
CitationJournal: 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
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5578
Polymers27,4172
Non-polymers4,1416
Water4,432246
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6662
Polymers13,7081
Non-polymers9571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8926
Polymers13,7081
Non-polymers3,1835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.631, 32.512, 71.879
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

21B-326-

HOH

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Components

#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-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O28V10
#3: Chemical ChemComp-FJF / 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#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.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 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 Pseudouridine Vanadate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 2, 2024 / Details: Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→29.17 Å / Num. obs: 22942 / % possible obs: 28.2 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.045 / Net I/σ(I): 10.57
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.80.16113980.9560.22181
1.8-1.920.0469030.9960.0651
1.92-2.080.03312390.9950.0471
2.08-2.280.02611190.9970.0371
2.28-2.540.02510240.9980.0361
2.54-2.940.0288960.9970.0391
2.94-3.590.0217750.9980.031
3.59-5.060.0316210.9960.0441
5.06-29.170.0433260.9950.0611

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.17 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 3695 8.66 %
Rwork0.1675 --
obs0.1707 42688 85.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 171 246 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082352
X-RAY DIFFRACTIONf_angle_d0.9854057
X-RAY DIFFRACTIONf_dihedral_angle_d12.157828
X-RAY DIFFRACTIONf_chiral_restr0.053290
X-RAY DIFFRACTIONf_plane_restr0.008343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.8786320.6828300X-RAY DIFFRACTION18
1.72-1.740.6456520.6254620X-RAY DIFFRACTION34
1.74-1.770.4572780.497693X-RAY DIFFRACTION42
1.77-1.790.4234960.378962X-RAY DIFFRACTION53
1.79-1.820.37621000.30081039X-RAY DIFFRACTION60
1.82-1.850.22971180.25541209X-RAY DIFFRACTION70
1.85-1.880.2241440.21221449X-RAY DIFFRACTION82
1.88-1.920.27961470.18551601X-RAY DIFFRACTION91
1.92-1.960.24111690.16981716X-RAY DIFFRACTION98
1.96-20.21351590.16951718X-RAY DIFFRACTION99
2-2.040.18731610.16511761X-RAY DIFFRACTION99
2.04-2.090.24311610.16751750X-RAY DIFFRACTION99
2.09-2.140.22931600.16481692X-RAY DIFFRACTION99
2.14-2.20.20861630.15561773X-RAY DIFFRACTION99
2.2-2.260.19431650.15921735X-RAY DIFFRACTION99
2.26-2.330.18451570.15031750X-RAY DIFFRACTION99
2.33-2.420.17791610.1511689X-RAY DIFFRACTION98
2.42-2.510.19821610.1481741X-RAY DIFFRACTION98
2.51-2.630.17241650.15031702X-RAY DIFFRACTION98
2.63-2.770.20511510.15411759X-RAY DIFFRACTION98
2.77-2.940.21471650.15641701X-RAY DIFFRACTION98
2.94-3.170.18231740.16011719X-RAY DIFFRACTION99
3.17-3.490.17291640.15221741X-RAY DIFFRACTION99
3.49-3.990.16851650.14381750X-RAY DIFFRACTION99
3.99-5.020.17441620.13411700X-RAY DIFFRACTION99
5.02-29.170.24011650.21811723X-RAY DIFFRACTION97
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)
10.7952-0.48780.09170.7451-0.0370.58770.09760.42120.032-0.2918-0.00070.16960.2601-0.0070.01930.1714-0.0314-0.03480.18990.00410.1081-33.161-19.72143.2237
21.02020.2915-0.10940.74760.43641.1247-0.06120.10580.1024-0.09040.03930.1194-0.0690.0514-0.0110.0609-0.0108-0.00820.04580.00580.062-30.2906-14.796113.2363
31.1021-0.38810.57650.1754-0.07070.7687-0.04210.03720.26950.07540.0589-0.091-0.3668-0.0043-0.13490.12140.01330.00350.0783-0.01090.0924-16.2334-9.290230.7446
40.6117-0.40120.0860.2768-0.01120.51650.00350.44590.0531-0.2324-0.0849-0.16580.1001-0.0154-0.01640.17320.02920.03130.2309-0.02740.1524-9.5885-15.156420.7583
51.1742-0.1080.15580.8897-0.45240.82640.00750.13740.0246-0.1495-0.0715-0.15150.04770.1104-0.01790.06890.00820.0190.0458-0.01060.0995-8.9085-17.217534.6478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 42 )
2X-RAY DIFFRACTION2chain 'B' and (resid 43 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 12 )
4X-RAY DIFFRACTION4chain 'A' and (resid 13 through 42 )
5X-RAY DIFFRACTION5chain 'A' and (resid 43 through 124 )

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