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- PDB-8zw3: Solution structure of TMPRSS2 promoter G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 8zw3
TitleSolution structure of TMPRSS2 promoter G-quadruplex
ComponentsDNA (5'-D(*TP*CP*TP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*C)-3')
KeywordsDNA / TMPRSS2 promoter / G-quadruplex / NMR solution structure
Function / homologyBERBERINE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsWang, K.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82322065 China
CitationJournal: To Be Published
Title: NMR Solution Structure of the Major TMPRSS2 Promoter G-Quadruplex and Its Complex with Berberine
Authors: Tang, Z.Y. / Li, S.R. / Bian, Y.T. / Chen, Z.Y. / Wang, Y.Y. / Zhang, Y.Q. / Li, Y.P. / Liu, Y.S. / Yang, M.H. / Kong, L.Y. / Wang, K.B.
History
DepositionJun 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: DNA (5'-D(*TP*CP*TP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9173
Polymers7,2451
Non-polymers6732
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*C)-3')


Mass: 7244.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-BER / BERBERINE


Mass: 336.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H NOESY
221anisotropic12D 1H-1H NOESY
331anisotropic12D 1H-1H NOESY
241anisotropic12D 1H-13C HSQC
351anisotropic12D 1H-13C HSQC
361anisotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 1.93 mM None BER-TMPRSS2_Pu23m3, 90% H2O/10% D2O / Label: none / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.93 mM / Component: BER-TMPRSS2_Pu23m3 / Isotopic labeling: None
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMConditions_171 atm288 K
210 mMConditions_271 atm298 K
310 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYWoonghee Leepeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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