[English] 日本語
Yorodumi
- PDB-6e80: Crystal structure of the Corn aptamer in unliganded state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+80
TitleCrystal structure of the Corn aptamer in unliganded state
ComponentsRNA (36-MER)
KeywordsRNA / polyribonucleotide / fluorigenic aptamer / G-quadruplex / apo
Function / homologyACETATE ION / : / IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 Å
AuthorsSjekloca, L. / Ferre-D'Amare, A.R.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.
Authors: Sjekloca, L. / Ferre-D'Amare, A.R.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,31613
Polymers11,7941
Non-polymers1,52212
Water362
1
A: RNA (36-MER)
hetero molecules

A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,63226
Polymers23,5882
Non-polymers3,04424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)93.012, 93.012, 66.560
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
11A-112-

IR

-
Components

-
RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (36-MER)


Mass: 11794.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 14 molecules

#2: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ir
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.42 Å3/Da / Density % sol: 49.17 % / Description: rectangular plate-shaped
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 0.2 M ammonium acetate pH 6.7, sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.10503 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10503 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 3961 / % possible obs: 89.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 52.61 Å2 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.109 / Rrim(I) all: 0.184 / Χ2: 5.001 / Net I/σ(I): 8.4 / Num. measured all: 8472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.441.30.4551340.7390.4550.6440.60463.5
2.44-2.491.40.5261550.5850.5210.7410.68269.8
2.49-2.531.50.5141850.5170.4840.7080.73580.4
2.53-2.591.80.7071650.1450.580.9190.72280.5
2.59-2.641.70.771860.5110.6291.0010.984.9
2.64-2.71.90.4741800.7120.3720.6060.77784.5
2.7-2.771.80.4841990.6980.4080.6370.83885.4
2.77-2.851.90.441900.8110.3530.5670.95393.1
2.85-2.9320.4172110.7360.3340.5370.79992.1
2.93-3.022.40.3562120.8470.2510.4381.23494.6
3.02-3.132.40.2422070.8840.1770.3022.24896.7
3.13-3.262.40.2312120.9540.1590.2812.75696.8
3.26-3.412.50.1712070.9720.1270.2142.78992.4
3.41-3.582.30.1482140.9730.1120.1862.85396
3.58-3.812.30.142120.9570.1040.1753.46797.2
3.81-4.12.50.1352270.9340.0990.1684.90597.8
4.1-4.522.50.1122120.9720.0820.144.88295.9
4.52-5.172.40.0932140.9780.0710.1185.61495.1
5.17-6.512.50.0932200.9720.0690.1168.26794.8
6.51-502.40.142190.9380.10.17330.37789.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å46.51 Å
Translation2.4 Å46.51 Å

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+81 / Resolution: 2.901→46.506 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 33.34
RfactorNum. reflection% reflection
Rfree0.3071 401 9.86 %
Rwork0.2524 --
obs0.2575 4068 85.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.92 Å2 / Biso mean: 48.8336 Å2 / Biso min: 25.55 Å2
Refinement stepCycle: final / Resolution: 2.901→46.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 762 36 2 800
Biso mean--61.16 38.04 -
Num. residues----35
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001878
X-RAY DIFFRACTIONf_angle_d0.2921384
X-RAY DIFFRACTIONf_chiral_restr0.019175
X-RAY DIFFRACTIONf_plane_restr0.00237
X-RAY DIFFRACTIONf_dihedral_angle_d12.365417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9009-3.32050.3051360.25051208134485
3.3205-4.18310.27051350.24611212134785
4.1831-46.5120.33371300.25721247137786
Refinement TLS params.Method: refined / Origin x: 15.1918 Å / Origin y: 60.3891 Å / Origin z: 26.9675 Å
111213212223313233
T0.2789 Å2-0.0437 Å20.0145 Å2-0.453 Å2-0.0732 Å2--0.3376 Å2
L2.874 °20.8669 °2-0.1169 °2-2.7529 °2-2.6408 °2--3.6548 °2
S0.0255 Å °-0.6737 Å °0.1916 Å °-0.0286 Å °-0.1524 Å °-0.0385 Å °0.2144 Å °0.3927 Å °0.3963 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 36
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allC2 - 3
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allE6
7X-RAY DIFFRACTION1allF2 - 3
8X-RAY DIFFRACTION1allG1
9X-RAY DIFFRACTION1allG2
10X-RAY DIFFRACTION1allI1
11X-RAY DIFFRACTION1allI2

+
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://pdbjlc1.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