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- PDB-8wa4: Solution structure of free ATF4 promoter G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 8wa4
TitleSolution structure of free ATF4 promoter G-quadruplex
ComponentsDNA G-quadruplex
KeywordsDNA / ATF4 promoter / G-quadruplex / NMR solution structure / glutamine-restricted cancer
Function / homology2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / THYMIDINE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsLiu, Y.S. / Wang, K.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173707 China
CitationJournal: To Be Published
Title: Stabilizing ATF4 promoter G-quadruplex overcomes the resistance of glutamine-restricted cancer therapy
Authors: Xiao, C.M. / Li, Y.P. / Liu, Y.S. / Dong, R.F. / He, X.Y. / Lin, Q. / Zang, X. / Wang, K.B. / Xia, Y.Z. / Kong, L.Y.
History
DepositionSep 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA G-quadruplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9773
Polymers6,4271
Non-polymers5492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA G-quadruplex


Mass: 6427.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
351isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 1.68 mM None ATF4_Pu22T, 90% H2O/10% D2O / Label: none / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.68 mM / Component: ATF4_Pu22T / Isotopic labeling: None
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMConditions_171 atm298 K
250 mMConditions_271 atm288 K
350 mMConditions_371 atm308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz / Details: QCI cryoprobe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYWoonghee Leepeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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