[English] 日本語
Yorodumi
- PDB-8u5p: Structure of Mango II aptamer bound to T01-6A-B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u5p
TitleStructure of Mango II aptamer bound to T01-6A-B
ComponentsMango II
KeywordsRNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPassalacqua, L.F.M. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Structure of Mango II aptamer bound to T01-6A-B
Authors: Passalacqua, L.F.M. / Ferre-D'Amare, A.R.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mango II
B: Mango II
C: Mango II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,01713
Polymers35,8093
Non-polymers1,20810
Water1267
1
A: Mango II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9105
Polymers11,9361
Non-polymers9734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mango II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0544
Polymers11,9361
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mango II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0544
Polymers11,9361
Non-polymers1173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.212, 183.720, 108.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-103-

K

-
Components

#1: RNA chain Mango II


Mass: 11936.274 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-VKI / 3-[2,16-dioxo-20-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)-6,9,12-trioxa-3,15-diazaicosan-1-yl]-2-{(E)-[6-(4-methoxyphenyl)-1-methylquinolin-4(1H)-ylidene]methyl}-1,3-benzothiazol-3-ium


Mass: 856.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H55N6O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: HEPES sodium, polyethylene glycol 400, and ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.10306 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10306 Å / Relative weight: 1
ReflectionResolution: 2.9→34.56 Å / Num. obs: 8556 / % possible obs: 98.34 % / Redundancy: 6.8 % / Biso Wilson estimate: 72.22 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.76
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 840 / CC1/2: 0.761

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→34.56 Å / SU ML: 0.3164 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 855 10.04 %
Rwork0.2128 7665 -
obs0.2158 8520 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.86 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2325 42 7 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152656
X-RAY DIFFRACTIONf_angle_d0.44754149
X-RAY DIFFRACTIONf_chiral_restr0.0228528
X-RAY DIFFRACTIONf_plane_restr0.0021108
X-RAY DIFFRACTIONf_dihedral_angle_d18.61651272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.080.30991410.29341267X-RAY DIFFRACTION99.72
3.08-3.320.26431400.22321247X-RAY DIFFRACTION98.23
3.32-3.650.23841400.22171239X-RAY DIFFRACTION97.87
3.65-4.180.25241400.22721278X-RAY DIFFRACTION98.61
4.18-5.260.22161450.211302X-RAY DIFFRACTION99.52
5.27-34.560.191490.191332X-RAY DIFFRACTION96.67
Refinement TLS params.Method: refined / Origin x: 19.4621953355 Å / Origin y: 25.6553142576 Å / Origin z: -3.73988150292 Å
111213212223313233
T0.47427989746 Å2-0.0190537204296 Å20.0415057320612 Å2-0.612275946046 Å20.101408015637 Å2--0.613279987831 Å2
L2.1544167088 °2-0.436932033175 °20.00164222369825 °2-0.882582659611 °2-0.193107139115 °2--1.8870562052 °2
S-0.0534667938368 Å °-0.423939303303 Å °-0.530666118307 Å °0.0795561929091 Å °0.0459155373327 Å °-0.00944065331495 Å °0.483893278137 Å °-0.0708139123993 Å °-0.0117165031415 Å °
Refinement TLS groupSelection details: all

+
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