[English] 日本語
Yorodumi
- PDB-8cto: Solution NMR structure of 8-residue Rosetta-designed cyclic pepti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cto
TitleSolution NMR structure of 8-residue Rosetta-designed cyclic peptide D8.31 in d6-DMSO with cis/trans switching (B-CT conformation)
ComponentsCyclic peptide D8.31 DAL-DPR-MLU-DVA-DAL-DPR-MLU-DVA
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
DepositionMay 16, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclic peptide D8.31 DAL-DPR-MLU-DVA-DAL-DPR-MLU-DVA


Theoretical massNumber of molelcules
Total (without water)8071
Polymers8071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cyclic peptide with two conformations observed in noesy data. A-CC (50%) and B-CT (50%). This one is B-CT conformation.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

-
Components

#1: Polypeptide(D) Cyclic peptide D8.31 DAL-DPR-MLU-DVA-DAL-DPR-MLU-DVA


Mass: 807.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

DetailsType: solution / Contents: 6 mg/mL peptide, 0.03 % TMS, DMSO / Details: D8.31-DMSO / Label: peptide / Solvent system: DMSO
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

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert , Mumenthaler, and Wuthrichrefinement
NMRFAM-SPARKY1.37Lee, Tonelli, Markleypeak picking
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin4.0.9Bruker Biospindata analysis
PdbStat5.21.6Tejero, Snyder, Mao, Aramini, Montelionedata analysis
CYANA3.98.13Guntert , Mumenthaler, and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 1
Details: This is conformation B (CT) of the 8-residue cyclic peptide present in the same NMR sample in d6-DMSO. A-CC conformation (50%) has cis MLU-3 and cis MLU-7 (pdb 7UBD) and B-CT (50%) ...Details: This is conformation B (CT) of the 8-residue cyclic peptide present in the same NMR sample in d6-DMSO. A-CC conformation (50%) has cis MLU-3 and cis MLU-7 (pdb 7UBD) and B-CT (50%) conformation has cis MLU-3 and trans MLU-7
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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