[English] 日本語
Yorodumi
- PDB-1emz: SOLUTION STRUCTURE OF FRAGMENT (350-370) OF THE TRANSMEMBRANE DOM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1emz
TitleSOLUTION STRUCTURE OF FRAGMENT (350-370) OF THE TRANSMEMBRANE DOMAIN OF HEPATITIS C ENVELOPE GLYCOPROTEIN E1
ComponentsENVELOPE GLYCOPROTEIN E1
KeywordsVIRAL PROTEIN / transmembrane domain / envelope protein E1 / hepatitis C virus
Function / homology
Function and homology information


host cell lipid droplet / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamic, energy minimization
AuthorsOp De Beeck, A. / Montserret, R. / Duvet, S. / Cocquerel, L. / Cacan, R. / Barberot, B. / Le Maire, M. / Penin, F. / Dubuisson, J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The transmembrane domains of hepatitis C virus envelope glycoproteins E1 and E2 play a major role in heterodimerization.
Authors: Op De Beeck, A. / Montserret, R. / Duvet, S. / Cocquerel, L. / Cacan, R. / Barberot, B. / Le Maire, M. / Penin, F. / Dubuisson, J.
History
DepositionMar 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN E1


Theoretical massNumber of molelcules
Total (without water)2,2381
Polymers2,2381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide ENVELOPE GLYCOPROTEIN E1


Mass: 2237.581 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN (RESIDUES 350-370) / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide is naturally found in hepatitis C virus.
References: UniProt: Q9Q3N3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
1312D NOESY
NMR detailsText: sodium 2,2 dimethyl-2-silapentane-5-sulfonate (DSS) in the internal nmr reference

-
Sample preparation

DetailsContents: 4 mM E1(350-370), 50% H2O, 50% D2 trifluoroethanol (v/v)
Solvent system: 50% H2O, 50% D2 trifluoroethanol (v/v)
Sample conditionspH: 5.7 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inc.collection
X-PLOR3.1Brunger A.T.structure solution
X-PLOR3.1Brunger A.T.refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamic, energy minimization
Software ordinal: 1
Details: the structure is based on 337 Noe derived distance constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 1

+
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