[English] 日本語
Yorodumi
- PDB-6ol3: Crystal structure of an adenovirus virus-associated RNA -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more