[English] 日本語
Yorodumi
- PDB-9aur: Crystal structure of loop-closed A21 2'-OMe dumbbell RNA bridged ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9aur
TitleCrystal structure of loop-closed A21 2'-OMe dumbbell RNA bridged by glycine
Components
  • Fab BL3-6 heavy chain
  • Fab BL3-6 light chain
  • Loop-closed A21 2'-OMe dumbbell RNA bridged by glycine
KeywordsRNA / RNA aminoacylation / T-loop / glycine-bridged flexizyme
Function / homologyGLYCINE / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRadakovic, A. / Lewicka, A. / Todisco, M. / Aitken, H.R.M. / Weiss, Z. / Kim, S. / Bannan, A. / Piccirilli, J.A. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149336 United States
Simons Foundation290363 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A potential role for RNA aminoacylation prior to its role in peptide synthesis.
Authors: Radakovic, A. / Lewicka, A. / Todisco, M. / Aitken, H.R.M. / Weiss, Z. / Kim, S. / Bannan, A. / Piccirilli, J.A. / Szostak, J.W.
History
DepositionFeb 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab BL3-6 heavy chain
L: Fab BL3-6 light chain
R: Loop-closed A21 2'-OMe dumbbell RNA bridged by glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7944
Polymers54,7193
Non-polymers751
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-31 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.466, 83.126, 73.339
Angle α, β, γ (deg.)90.000, 90.250, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody Fab BL3-6 heavy chain


Mass: 24181.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab BL3-6 light chain


Mass: 23394.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: RNA chain Loop-closed A21 2'-OMe dumbbell RNA bridged by glycine


Mass: 7142.382 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.07 M Citric Acid; 0.03 M BIS-TRIS Propane; 16% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.57→54.99 Å / Num. obs: 65261 / % possible obs: 96.43 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.94 Å2 / CC1/2: 0.903 / Net I/σ(I): 9.31
Reflection shellResolution: 1.57→1.626 Å / Num. unique obs: 6414 / CC1/2: 0.488

-
Processing

Software
NameVersionClassification
PHASER1.20.1_4487phasing
PHENIX1.20.1_4487refinement
MOSFLM1.20.1_4487data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→54.99 Å / SU ML: 0.179 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.4932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.212 1995 3.13 %
Rwork0.186 61709 -
obs0.1868 63704 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.23 Å2
Refinement stepCycle: LAST / Resolution: 1.57→54.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 477 4 626 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633958
X-RAY DIFFRACTIONf_angle_d0.99275481
X-RAY DIFFRACTIONf_chiral_restr0.0565631
X-RAY DIFFRACTIONf_plane_restr0.0066616
X-RAY DIFFRACTIONf_dihedral_angle_d12.91221478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.27521380.27524413X-RAY DIFFRACTION97.47
1.61-1.650.27461440.25274484X-RAY DIFFRACTION98.2
1.65-1.70.25121400.24354478X-RAY DIFFRACTION97.67
1.7-1.760.2441360.25964244X-RAY DIFFRACTION93.71
1.76-1.820.26711470.23524447X-RAY DIFFRACTION97.23
1.82-1.890.24091460.21034473X-RAY DIFFRACTION97.96
1.89-1.980.22351430.20234301X-RAY DIFFRACTION93.93
1.98-2.080.2331480.19924393X-RAY DIFFRACTION96.64
2.08-2.210.22851450.18654452X-RAY DIFFRACTION97.79
2.21-2.380.2351470.18894422X-RAY DIFFRACTION96.68
2.38-2.620.22281410.18584464X-RAY DIFFRACTION96.89
2.62-30.2081420.18484437X-RAY DIFFRACTION97.18
3-3.780.19821400.16454327X-RAY DIFFRACTION94.3
3.78-54.990.1681380.15554374X-RAY DIFFRACTION93.63

+
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