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- PDB-6ol3: Crystal structure of an adenovirus virus-associated RNA -

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Basic information

Entry
Database: PDB / ID: 6ol3
TitleCrystal structure of an adenovirus virus-associated RNA
ComponentsAdenovirus Virus-Associated (VA) RNA I apical and central domains
KeywordsRNA / noncoding RNA / viral RNA
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHuman adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsHood, I.V. / Gordon, J.M. / Bou-Nader, C. / Henderson, F.V. / Bahmanjah, S. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK075136-03 United States
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structure of an adenovirus virus-associated RNA.
Authors: Hood, I.V. / Gordon, J.M. / Bou-Nader, C. / Henderson, F.E. / Bahmanjah, S. / Zhang, J.
History
DepositionApr 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Adenovirus Virus-Associated (VA) RNA I apical and central domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1622
Polymers36,1221
Non-polymers391
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.455, 100.455, 130.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: RNA chain Adenovirus Virus-Associated (VA) RNA I apical and central domains


Mass: 36122.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 4.56 Å3/Da / Density % sol: 73.05 % / Description: obelisk crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM sodium cacodylate (pH 6.5) 28-30% 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 22, 2016
RadiationMonochromator: MD2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→40 Å / Num. obs: 18246 / % possible obs: 99.9 % / Observed criterion σ(F): 0.82 / Redundancy: 8.2 %
Data reduction details: EDS server used different resolution to calculate completeness. The higher Rmerge is partly due to the higher redundancy
Rmerge(I) obs: 0.152 / Net I/σ(I): 12.2
Reflection shellResolution: 2.74→2.81 Å / Redundancy: 8.2 % / Rmerge(I) obs: 3.642 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 1310 / CC1/2: 0.34 / Rrim(I) all: 3.884 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.74→39.824 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.2353 2635 7.89 %
Rwork0.2174 --
obs0.2188 18173 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.74→39.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2352 1 9 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022625
X-RAY DIFFRACTIONf_angle_d0.414089
X-RAY DIFFRACTIONf_dihedral_angle_d11.8861324
X-RAY DIFFRACTIONf_chiral_restr0.022553
X-RAY DIFFRACTIONf_plane_restr0.002109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.78980.44281310.43821564X-RAY DIFFRACTION94
2.7898-2.84350.41271320.431563X-RAY DIFFRACTION97
2.8435-2.90150.44631400.40281598X-RAY DIFFRACTION100
2.9015-2.96460.33651440.36091639X-RAY DIFFRACTION100
2.9646-3.03350.33921390.30911623X-RAY DIFFRACTION100
3.0335-3.10930.26311410.25421617X-RAY DIFFRACTION100
3.1093-3.19340.24611360.23031621X-RAY DIFFRACTION100
3.1934-3.28730.26961360.21531642X-RAY DIFFRACTION100
3.2873-3.39330.25941380.20551616X-RAY DIFFRACTION100
3.3933-3.51460.22811400.23571626X-RAY DIFFRACTION100
3.5146-3.65520.23771450.23051629X-RAY DIFFRACTION100
3.6552-3.82140.24081340.17961620X-RAY DIFFRACTION100
3.8214-4.02270.20171410.1791639X-RAY DIFFRACTION100
4.0227-4.27450.22841410.19641601X-RAY DIFFRACTION100
4.2745-4.6040.19321440.20891641X-RAY DIFFRACTION100
4.604-5.06650.20511320.18551631X-RAY DIFFRACTION100
5.0665-5.79780.20781370.18561626X-RAY DIFFRACTION100
5.7978-7.29720.2461410.19371625X-RAY DIFFRACTION100
7.2972-39.82820.18051430.18761626X-RAY DIFFRACTION99
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)
1-0.06830.31230.19290.1350.05360.0494-0.13650.178-0.3197-0.40250.3085-0.4350.54250.0688-0.17491.5072-0.04860.02810.8142-0.18210.652-35.903517.2138-14.9106
20.96910.1703-0.04170.64160.06134.23580.16490.1190.0336-0.21030.0222-0.1130.10850.5585-0.16040.59010.00160.04490.6438-0.01720.2473-34.338751.53640.97
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 26 through 87 )
2X-RAY DIFFRACTION2chain 'C' and (resid 88 through 137 )

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