[English] 日本語
Yorodumi
- PDB-7sxp: G-quadruplex structure formed in the NRAS mRNA with a G8U substitution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7sxp
TitleG-quadruplex structure formed in the NRAS mRNA with a G8U substitution
ComponentsNRAS mRNA
KeywordsRNA / G-quadruplex / NRAS
Function / homologyCACODYLIC ACID / : / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBanco, M.T. / 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: Cell Chem Biol / Year: 2023
Title: Investigating the NRAS 5' UTR as a target for small molecules.
Authors: Balaratnam, S. / Torrey, Z.R. / Calabrese, D.R. / Banco, M.T. / Yazdani, K. / Liang, X. / Fullenkamp, C.R. / Seshadri, S. / Holewinski, R.J. / Andresson, T. / Ferre-D'Amare, A.R. / ...Authors: Balaratnam, S. / Torrey, Z.R. / Calabrese, D.R. / Banco, M.T. / Yazdani, K. / Liang, X. / Fullenkamp, C.R. / Seshadri, S. / Holewinski, R.J. / Andresson, T. / Ferre-D'Amare, A.R. / Incarnato, D. / Schneekloth Jr., J.S.
History
DepositionNov 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NRAS mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6366
Polymers7,2421
Non-polymers3935
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.402, 36.402, 70.103
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

-
Components

#1: RNA chain NRAS mRNA


Mass: 7242.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 - 25 % PEG 3350, 80 mM sodium chloride and 100 mM BIS-TRIS pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.104 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 2.3→31.53 Å / Num. obs: 2556 / % possible obs: 99.6 % / Redundancy: 17.4 % / Biso Wilson estimate: 88.13 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.058 / Net I/σ(I): 5.3
Reflection shellResolution: 2.32→2.42 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 305 / CC1/2: 0.468 / Rpim(I) all: 0.678

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
PHENIX1.19.2_4158phasing
pointlessdata scaling
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→31.53 Å / SU ML: 0.1496 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.7152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2772 61 4.58 %
Rwork0.2408 1270 -
obs0.2421 1331 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 13 0 425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031468
X-RAY DIFFRACTIONf_angle_d0.6193732
X-RAY DIFFRACTIONf_chiral_restr0.045996
X-RAY DIFFRACTIONf_plane_restr0.006517
X-RAY DIFFRACTIONf_dihedral_angle_d19.3227223
LS refinement shellResolution: 2.9→31.53 Å
RfactorNum. reflection% reflection
Rfree0.2772 61 -
Rwork0.2408 1270 -
obs--98.37 %

+
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