[English] 日本語
Yorodumi
- PDB-6d3p: Crystal structure of an exoribonuclease-resistant RNA from Sweet ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d3p
TitleCrystal structure of an exoribonuclease-resistant RNA from Sweet clover necrotic mosaic virus (SCNMV)
ComponentsRNA (45-MER)
KeywordsRNA / RNA maturation / exoribonuclease resistance / viral non-coding RNA
Function / homologyIRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesSweet clover necrotic mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsSteckelberg, A.-L. / Akiyama, B.M. / Costantino, D.A. / Sit, T.L. / Nix, J.C. / Kieft, J.S.
Funding support United States, European Union, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118070 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI133348 United States
European Molecular Biology Organization (EMBO)ALTF 611-2015European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM117730 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA046934 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.
Authors: Steckelberg, A.L. / Akiyama, B.M. / Costantino, D.A. / Sit, T.L. / Nix, J.C. / Kieft, J.S.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.3Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Mar 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
A: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,48811
Polymers14,5441
Non-polymers2,94410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: RNA (45-MER)
hetero molecules

A: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,97522
Polymers29,0872
Non-polymers5,88820
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area8490 Å2
ΔGint-55 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.400, 83.400, 94.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: RNA chain RNA (45-MER)


Mass: 14543.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcribed with T7 RNA polymerase / Source: (synth.) Sweet clover necrotic mosaic virus
#2: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H18IrN6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: drop: 1 uL 5 mg/mL RNA in 30 mM HEPES pH 7.5, 20 mM MgCl2, 100 mM KCl + 1 uL 50 mM sodium cacodylate trihydrate (pH 6.5), 0.2 M potassium chloride, 0.1 M magnesium acetate tetrahydrate, 14% ...Details: drop: 1 uL 5 mg/mL RNA in 30 mM HEPES pH 7.5, 20 mM MgCl2, 100 mM KCl + 1 uL 50 mM sodium cacodylate trihydrate (pH 6.5), 0.2 M potassium chloride, 0.1 M magnesium acetate tetrahydrate, 14% w/v PEG 8000. Crystals were buffer-exchanged into freezing solution (mother liquor containing 20% ethylene glycol and 20 mM Iridium (III) hexammine) and flash-frozen in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0972 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 1.85→39.455 Å / Num. obs: 27657 / % possible obs: 88.6 % / Redundancy: 25.782 % / Biso Wilson estimate: 94.26 Å2 / CC1/2: 0.884 / Rmerge(I) obs: 0.592 / Rrim(I) all: 0.612 / Χ2: 1.754 / Net I/σ(I): 7.14 / Num. measured all: 713044 / Scaling rejects: 1073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured obsNum. possibleNum. unique obs% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRrim(I) all
1.85-1.91.696919228854223.7
1.9-1.952.57233572236130558.40.15
1.95-2.013.90269102192177180.8
2.01-2.075.0697202126192190.4
2.07-2.146.348122702074193393.2
2.14-2.219.409180471981191896.8
2.21-2.313.761261871925190398.9
2.3-2.3920.202374751857185599.9
2.39-2.527.197481391772177099.9
2.5-2.6237.557636961705169699.50.147
2.62-2.7641.623665131601159899.80.338
2.76-2.9341.56633371530152499.60.670.708
2.93-3.1341.069589341438143599.81.670.8254.084.131
3.13-3.3843.06257617133813381004.420.9711.5121.53
3.38-3.746.612570071223122310010.870.9960.5750.581
3.7-4.1446.959520771109110910020.760.9980.2910.294
4.14-4.7847.024631598598510032.8510.1460.148
4.78-5.8646.8963873682682610053.6510.0830.084
5.86-8.2846.6033019964864810071.8410.0620.063
8.28-39.45543.6671558936335798.381.5510.0540.054

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
AutoSolphasing
RefinementResolution: 2.9→39.455 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.09
RfactorNum. reflection% reflection
Rfree0.2587 816 10.07 %
Rwork0.2415 --
obs0.2434 8106 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 280.9 Å2 / Biso mean: 95.3912 Å2 / Biso min: 52.7 Å2
Refinement stepCycle: final / Resolution: 2.9→39.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 966 70 0 1036
Biso mean--130.39 --
Num. residues----45
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9002-3.08190.41811320.376812281360100
3.0819-3.31970.31161400.30981199133999
3.3197-3.65360.3551380.280112091347100
3.6536-4.18170.27771340.24241217135199
4.1817-5.26660.25261380.234912161354100
5.2666-39.45910.20361340.206512211355100

+
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