[English] 日本語
Yorodumi
- PDB-8ebo: Homopurine parallel G-quadruplex from human chromosome 7 stabiliz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ebo
TitleHomopurine parallel G-quadruplex from human chromosome 7 stabilized by K+ ions
ComponentsDNA (5'-D(*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*A)-3')
KeywordsDNA / G-quadruplex / parallel / propeller loops
Function / homologyCOBALT (III) ION / : / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChen, E.V. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Homopurine guanine-rich sequences in complex with N-methyl mesoporphyrin IX form parallel G-quadruplex dimers and display a unique symmetry tetrad.
Authors: Ye, M. / Chen, E.V. / Pfeil, S.H. / Martin, K.N. / Atrafi, T. / Yun, S. / Martinez, Z. / Yatsunyk, L.A.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8276
Polymers7,0701
Non-polymers7575
Water724
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)42.053, 47.474, 119.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-105-

3CO

21A-202-

HOH

-
Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*A)-3')


Mass: 7069.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-3CO / COBALT (III) ION / Cobalt


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: thin, well-ordered rhombuses
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop
Details: The well condition included 0.012 M NaCl, 0.08-0.1 M KCl, 0.04 M sodium cacodylate pH 5.5, 45% MPD, and 0.002 M hexammine cobalt(III) chloride

-
Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→30.44 Å / Num. obs: 4296 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 64.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.054 / Net I/σ(I): 15.1
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 279 / CC1/2: 0.351 / Rpim(I) all: 0.894 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimlessdata scaling
Coot0.8.9.2model building
PHENIX1.19.2_4158phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0F

4g0f


Resolution: 1.98→24.71 Å / SU ML: 0.2268 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.9448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 425 9.99 %
Rwork0.2314 3829 -
obs0.2362 4254 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.26 Å2
Refinement stepCycle: LAST / Resolution: 1.98→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 435 37 4 476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142530
X-RAY DIFFRACTIONf_angle_d1.9337823
X-RAY DIFFRACTIONf_chiral_restr0.068682
X-RAY DIFFRACTIONf_plane_restr0.012823
X-RAY DIFFRACTIONf_dihedral_angle_d36.279203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.270.35661380.29661242X-RAY DIFFRACTION97.87
2.27-2.850.3471410.36191278X-RAY DIFFRACTION99.51
2.86-24.710.26121460.20421309X-RAY DIFFRACTION96.94
Refinement TLS params.Method: refined / Origin x: -15.0484741614 Å / Origin y: 2.8269384339 Å / Origin z: -14.539514764 Å
111213212223313233
T0.725036053306 Å2-0.254114679539 Å20.274254950121 Å2-0.545266786161 Å20.0258571795824 Å2--0.801844313619 Å2
L7.21771039797 °20.62766346869 °2-1.00812691194 °2-5.13867186864 °2-0.475429448416 °2--3.1501477118 °2
S-0.594130132333 Å °0.466286019956 Å °-0.875157920592 Å °-1.86782205107 Å °0.488663282853 Å °-2.13708530652 Å °0.645045189978 Å °0.702718040884 Å °0.380776529808 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