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- PDB-7ubi: Solution NMR structure of 8-residue Rosetta-designed cyclic pepti... -

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Basic information

Entry
Database: PDB / ID: 7ubi
TitleSolution NMR structure of 8-residue Rosetta-designed cyclic peptide D8.21 in CDCl3 with cis/trans switching (TT conformation, 47%)
ComponentsCyclic peptide D8.21 DVA-MLE-DPR-LEU-DVA-MLE-DPR-LEU
KeywordsDE NOVO PROTEIN / cyclic peptide / non natural amino acids / cis/trans / switch peptides / de novo design / membrane permeability
Function / homologypolypeptide(D)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / na
AuthorsRamelot, T.A. / Tejero, R. / Montelione, G.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141818 United States
CitationJournal: Cell / Year: 2022
Title: Accurate de novo design of membrane-traversing macrocycles.
Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / ...Authors: Bhardwaj, G. / O'Connor, J. / Rettie, S. / Huang, Y.H. / Ramelot, T.A. / Mulligan, V.K. / Alpkilic, G.G. / Palmer, J. / Bera, A.K. / Bick, M.J. / Di Piazza, M. / Li, X. / Hosseinzadeh, P. / Craven, T.W. / Tejero, R. / Lauko, A. / Choi, R. / Glynn, C. / Dong, L. / Griffin, R. / van Voorhis, W.C. / Rodriguez, J. / Stewart, L. / Montelione, G.T. / Craik, D. / Baker, D.
History
DepositionMar 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic peptide D8.21 DVA-MLE-DPR-LEU-DVA-MLE-DPR-LEU


Theoretical massNumber of molelcules
Total (without water)8911
Polymers8911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: noesy
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Polypeptide(D) Cyclic peptide D8.21 DVA-MLE-DPR-LEU-DVA-MLE-DPR-LEU


Mass: 891.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D 1H
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-13C HSQC-ed
151isotropic12D 1H-1H NOESY
161isotropic12D 1H-1H ROESY
171isotropic12D 1H-1H COSY
181isotropic12D 1H-1H TOCSY
191isotropic12D 1H-13C HMBC
1101isotropic12D 1H-13C HSQC -TOCSY

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Sample preparation

DetailsType: solution / Contents: 6 mg/mL peptide, 0.03 % TMS, CDCl3 / Label: D8.21-CDCl3 / Solvent system: CDCl3
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
6 mg/mLpeptidenatural abundance1
0.03 %TMSnatural abundance1
Sample conditionsIonic strength: NA Not defined / Label: conditions_1 / pH: 0.0 Not defined / Pressure: 1 atm / Temperature: 293 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: CP TCI - Pharaoh - RPI

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert P., Mumenthaler, and Wuthrichrefinement
NMRFAM-SPARKY1.37Lee, Tonelli, Markleypeak picking
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.5Bruker Biospindata analysis
PdbStat5.21.6Tejero, Snyder, Mao, Aramini, Montelionedata analysis
CYANA3.98.13Guntert P., Mumenthaler, and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 1
Details: This is conformation A (TT) of the same 8-residue cyclic peptide present in the same NMR sample. TT symmetric conformation has trans DPR3 and trans DPR7 (47%). TC conformation has trans DPR3 and cis DPR7 (53%).
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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