Journal: Nucleic Acids Res. / Year: 2010 Title: Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: ...Title: Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site Authors: Brown, K.L. / Roginskaya, M. / Zou, Y. / Altamirano, A. / Basu, A.K. / Stone, M.P.
back calculated data agree with experimental NOESY spectrum
Representative
Model #1
closest to the average
-
Components
#1: DNA chain
5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'
Mass: 3749.425 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain
5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'
Mass: 3609.398 Da / Num. of mol.: 1 / Source method: obtained synthetically
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR Details: When base paired with adenine Thymine glycol is in equilibrium between cis-5R,6S-TG and trans-5R,6R, TG. In addition, theCTG can pucker so that theCTG CH3 is in an axial or equatorial ...Details: When base paired with adenine Thymine glycol is in equilibrium between cis-5R,6S-TG and trans-5R,6R, TG. In addition, theCTG can pucker so that theCTG CH3 is in an axial or equatorial conformation. This entry is the cis-5R,6S-TG lesion opposite dA withCTG CH3 in an axial conformation
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-1H NOESY
1
2
1
2D 1H-1H COSY
2
3
2
2D 1H-1H NOESY
1
4
1
2D 31P-1H COSY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4, 100% D2O
100% D2O
2
20 mM sodium phosphate-5, 100 mM sodium chloride-6, 10 uM sodium azide-7, 50 uM EDTA-8, 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Solution-ID
20mM
sodium phosphate-1
1
100mM
sodium chloride-2
1
10uM
sodium azide-3
1
50uM
EDTA-4
1
20mM
sodium phosphate-5
2
100mM
sodium chloride-6
2
10uM
sodium azide-7
2
50uM
EDTA-8
2
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
0.1
7
ambient
303K
2
0.1
7
ambient
278K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
800
1
Bruker Avance
Bruker
AVANCE
600
2
-
Processing
NMR software
Name
Version
Developer
Classification
Amber
9
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollm
Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 10 / Conformers submitted total number: 10
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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