[English] 日本語
Yorodumi
- PDB-6pez: SOLID-STATE NMR STRUCTURE OF PISCIDIN 3 IN ALIGNED 4:1 PHOSPHATID... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pez
TitleSOLID-STATE NMR STRUCTURE OF PISCIDIN 3 IN ALIGNED 4:1 PHOSPHATIDYLCHOLINE/CHOLESTEROL LIPID BILAYERS
ComponentsPiscidin-3
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / ANTICANCER PEPTIDE / ANTI HIV-1 / CATIONIC / AMPHIPATHIC / HISTIDINE RICH / HELICAL / LIPID BILAYERS / BACTERIAL CELL MEMBRANE MIMIC
Function / homology
Function and homology information


regulation of defense response to virus / killing of cells of another organism / defense response to bacterium / innate immune response / lipid binding / extracellular region / membrane
Similarity search - Function
Pleurocidin / Pleurocidin family
Similarity search - Domain/homology
Biological speciesMorone chrysops x Morone saxatilis (white bass x striped sea-bass)
MethodSOLID-STATE NMR / simulated annealing
AuthorsGreenwood, A.I. / Cairns, L.S. / Fu, R. / Cotten, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1716608 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The host-defense peptide piscidin P1 reorganizes lipid domains in membranes and decreases activation energies in mechanosensitive ion channels.
Authors: Comert, F. / Greenwood, A. / Maramba, J. / Acevedo, R. / Lucas, L. / Kulasinghe, T. / Cairns, L.S. / Wen, Y. / Fu, R. / Hammer, J. / Blazyk, J. / Sukharev, S. / Cotten, M.L. / Mihailescu, M.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Piscidin-3


Theoretical massNumber of molelcules
Total (without water)2,4961
Polymers2,4961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area2380 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Piscidin-3


Mass: 2495.952 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Morone chrysops x Morone saxatilis (white bass x striped sea-bass)
References: UniProt: P0C006

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic315N 1H solid-state de-HETCOR
122anisotropic215N 1H solid-state de-HETCOR
133anisotropic215N 1H solid-state de-HETCOR
144anisotropic115N 1H solid-state de-HETCOR
159anisotropic115N 1H solid-state de-HETCOR
1168anisotropic115N 1H solid-state de-HETCOR
1157anisotropic215N 1H solid-state de-HETCOR
1146anisotropic315N 1H solid-state de-HETCOR
1135anisotropic215N 1H solid-state de-HETCOR
11210anisotropic215N 1H solid-state de-HETCOR
11111anisotropic215N 1H solid-state de-HETCOR
11012anisotropic315N 1H solid-state de-HETCOR
1913anisotropic315N 1H solid-state de-HETCOR
1814anisotropic315N 1H solid-state de-HETCOR

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
oriented membrane film110 mM [15N]-I2I5G8 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4I2-I5-G8-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film210 mM [15N]-V10G13I16 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4V10-G13-I16-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film310 mM [15N]-G17F19L20 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4G17-F19-L20-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film410 mM [15N]-F1S15 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4F1-S15-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film910 mM [15N]-F6I9 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4F6-I9-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film810 mM [15N]-F6I9A12 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4F6-I9-A12-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film710 mM [15N]-R18 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4R18-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film610 mM [15N]-H4 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H4-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film510 mM [15N]-R14 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4R14-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1010 mM [15N]-R7 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4R7-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1110 mM [15N]-T21G22 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4T21-G22-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1210 mM [15N]-H11 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H11-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1310 mM [15N]-H3 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4H3-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
oriented membrane film1410 mM [15N]-A12G17 PISCIDIN-3, 320 mM 1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholine, 80 mM Cholesterol, H2O 100%; phosphate buffer 40 mM pH 7.4A12-G17-15N_P3H2O 100%; phosphate buffer 40 mM pH 7.4
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMPISCIDIN-3[15N]-I2I5G81
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance1
80 mMCholesterolnatural abundance1
10 mMPISCIDIN-3[15N]-V10G13I162
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance2
80 mMCholesterolnatural abundance2
10 mMPISCIDIN-3[15N]-G17F19L203
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance3
80 mMCholesterolnatural abundance3
10 mMPISCIDIN-3[15N]-F1S154
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance4
80 mMCholesterolnatural abundance4
10 mMPISCIDIN-3[15N]-F6I99
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance9
80 mMCholesterolnatural abundance9
10 mMPISCIDIN-3[15N]-F6I9A128
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance8
80 mMCholesterolnatural abundance8
10 mMPISCIDIN-3[15N]-R187
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance7
80 mMCholesterolnatural abundance7
10 mMPISCIDIN-3[15N]-H46
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance6
80 mMCholesterolnatural abundance6
10 mMPISCIDIN-3[15N]-R145
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance5
80 mMCholesterolnatural abundance5
10 mMPISCIDIN-3[15N]-R710
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance10
80 mMCholesterolnatural abundance10
10 mMPISCIDIN-3[15N]-T21G2211
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance11
80 mMCholesterolnatural abundance11
10 mMPISCIDIN-3[15N]-H1112
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance12
80 mMCholesterolnatural abundance12
10 mMPISCIDIN-3[15N]-H313
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance13
80 mMCholesterolnatural abundance13
10 mMPISCIDIN-3[15N]-A12G1714
320 mM1-palmitoyl-2-oleoyl-sn-glycero-phosphatidylcholinenatural abundance14
80 mMCholesterolnatural abundance14
Sample conditionsIonic strength: 40 mM / Label: sample_conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 305 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Rennselaer Polytechnic Institute
Bruker AVANCEBrukerAVANCE9002National High Magnetic Field Laboratory
Bruker AVANCEBrukerAVANCE6003National High Magnetic Field Laboratory

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TopSpin2.1Bruker Biospincollection
XwinNMR3.5Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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.

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://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