[English] 日本語
Yorodumi
- PDB-8feo: 16mer self-complementary duplex RNA with two separated native U:U... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8feo
Title16mer self-complementary duplex RNA with two separated native U:U pairs
ComponentsRNA 16mer
KeywordsRNA / Duplexes / UU pairs
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsFang, Z. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Simons Foundation290363FY18 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying.
Authors: Ding, D. / Fang, Z. / Kim, S.C. / O'Flaherty, D.K. / Jia, X. / Stone, T.B. / Zhou, L. / Szostak, J.W.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: RNA 16mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1723
Polymers5,0601
Non-polymers1122
Water1,31573
1
AAA: RNA 16mer
hetero molecules

AAA: RNA 16mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3446
Polymers10,1202
Non-polymers2244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2040 Å2
ΔGint-81 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.503, 41.503, 125.299
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-222-

HOH

21AAA-238-

HOH

31AAA-248-

HOH

41AAA-259-

HOH

51AAA-260-

HOH

-
Components

#1: RNA chain RNA 16mer


Mass: 5060.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 1.52→17.8 Å / Num. obs: 6587 / % possible obs: 98.3 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Net I/σ(I): 36.4
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3 / Num. unique obs: 322 / CC1/2: 0.973 / Rpim(I) all: 0.093 / Rrim(I) all: 0.253 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→17.796 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.579 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2393 320 4.858 %
Rwork0.198 6267 -
all0.2 --
obs-6587 98.182 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20.004 Å2-0 Å2
2--0.008 Å2-0 Å2
3----0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.52→17.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 2 73 409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.012372
X-RAY DIFFRACTIONr_bond_other_d0.0030.018155
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.789577
X-RAY DIFFRACTIONr_angle_other_deg0.6881.655379
X-RAY DIFFRACTIONr_chiral_restr0.2260.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0280.02181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0258
X-RAY DIFFRACTIONr_nbd_refined0.0820.222
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.2141
X-RAY DIFFRACTIONr_nbtor_refined0.2380.2139
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.246
X-RAY DIFFRACTIONr_metal_ion_refined0.210.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.214
X-RAY DIFFRACTIONr_nbd_other0.4140.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.212
X-RAY DIFFRACTIONr_scbond_it1.7222.075371
X-RAY DIFFRACTIONr_scbond_other1.7192.073372
X-RAY DIFFRACTIONr_scangle_it2.3583.133577
X-RAY DIFFRACTIONr_scangle_other2.3563.132578
X-RAY DIFFRACTIONr_lrange_it4.6221.183490
X-RAY DIFFRACTIONr_lrange_other4.63620.143474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.229220.231451X-RAY DIFFRACTION99.1614
1.56-1.6020.212200.204454X-RAY DIFFRACTION100
1.602-1.6490.249280.206429X-RAY DIFFRACTION100
1.649-1.6990.219230.183417X-RAY DIFFRACTION100
1.699-1.7550.234180.181413X-RAY DIFFRACTION100
1.755-1.8160.293210.189408X-RAY DIFFRACTION100
1.816-1.8850.194220.194387X-RAY DIFFRACTION100
1.885-1.9620.279240.205362X-RAY DIFFRACTION99.4845
1.962-2.0490.218140.207367X-RAY DIFFRACTION100
2.049-2.1480.271160.22341X-RAY DIFFRACTION100
2.148-2.2640.318170.223331X-RAY DIFFRACTION100
2.264-2.4010.36180.191317X-RAY DIFFRACTION99.7024
2.401-2.5660.191150.192293X-RAY DIFFRACTION99.6764
2.566-2.7710.174170.22269X-RAY DIFFRACTION98.9619
2.771-3.0340.212130.167262X-RAY DIFFRACTION100
3.034-3.390.15650.179216X-RAY DIFFRACTION92.4686
3.39-3.910.295110.171195X-RAY DIFFRACTION94.0639
3.91-4.7790.212110.173169X-RAY DIFFRACTION90.9091
4.779-6.7140.22540.239126X-RAY DIFFRACTION86.0927
6.714-17.7960.35910.37760X-RAY DIFFRACTION59.8039

+
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://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