[English] 日本語
Yorodumi
- PDB-1erf: CONFORMATIONAL MAPPING OF THE N-TERMINAL FUSION PEPTIDE OF HIV-1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1erf
TitleCONFORMATIONAL MAPPING OF THE N-TERMINAL FUSION PEPTIDE OF HIV-1 GP41 USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY (FTIR)
ComponentsTRANSMEMBRANE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / human immunodeficiency virus (HIV-1) / viral fusion peptide / gp41
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
MethodINFRARED SPECTROSCOPY / molecular dynamics, simulated annealing
AuthorsGordon, L.M. / Mobley, P.W. / Pilpa, R. / Sherman, M.A. / Waring, A.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2002
Title: Conformational mapping of the N-terminal peptide of HIV-1 gp41 in membrane environments using (13)C-enhanced Fourier transform infrared spectroscopy.
Authors: Gordon, L.M. / Mobley, P.W. / Pilpa, R. / Sherman, M.A. / Waring, A.J.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSMEMBRANE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)2,1231
Polymers2,1231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 31structures with acceptable covalent geometry
RepresentativeModel #9closest to the average

-
Components

#1: Protein/peptide TRANSMEMBRANE GLYCOPROTEIN / GP41


Mass: 2123.481 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FUSION PEPTIDE (RESIDUES 519-541) / Mutation: C-TERMINUS HAS BEEN AMIDATED / Source method: obtained synthetically
Details: The sequence of this peptide occurs naturally in human immunodeficiency virus glycoprotein 41.
References: UniProt: P03377

-
Experimental details

-
Experiment

ExperimentMethod: INFRARED SPECTROSCOPY
NMR experimentType: 13-C isotope enhanced FTIR
NMR detailsText: The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information.

-
Sample preparation

CrystalDescription: This structure was determined by means of 13C-enhanced Fourier Transform Infrared Spectroscopy (FTIR). Data set consists of 17 conformers derived from simulated annealing with constraints from FTIR.
DetailsContents: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES ...Contents: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527,528,529,530,531,532,533,534,538,539.
Solvent system: 70% hexafluoroisopropanol (HFIP), 29.9% water, 0.1% formic acid (v/v)
Sample conditionsIonic strength: 0 / pH: 7.0 / Pressure: 1 atm / Temperature: 298
Crystal grow
*PLUS
Method: infrared spectroscopy

-
Data collection

NMR spectrometerType: Mattson FTIR Research Series / Manufacturer: Mattson FTIR / Model: Research Series / Field strength: 0 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
WinfirstFTIR curve fitting softwareKauppine et al.data analysis
DISCOVER2.9.7Molecular Simulations, Inc. (San Diego, CA)refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: Molecular dynamics (simulated annealing) was used to generate an ensemble of conformers consistent with the FTIR data.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 31 / Conformers submitted total number: 17

+
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