[English] 日本語
Yorodumi
- PDB-2h95: Structure of the Amantadine-Blocked Influenza A M2 Proton Channel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h95
TitleStructure of the Amantadine-Blocked Influenza A M2 Proton Channel Trans-membrane Domain by Solid-state NMR spectroscopy
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / ALPHA HELIX / PROTEIN-LIGAND
Function / homology
Function and homology information


: / suppression by virus of host autophagy / : / proton transmembrane transporter activity / protein complex oligomerization / monoatomic ion channel activity / structural constituent of virion / membrane => GO:0016020 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Matrix protein 2 / Matrix protein 2
Similarity search - Component
MethodSOLID-STATE NMR / ENERGY MINIMIZATION WITH ORIENTATIONAL CONSTRAINTS
AuthorsHu, J. / Asbury, T. / Cross, T.A.
CitationJournal: Biophys.J. / Year: 2007
Title: Backbone structure of the amantadine-blocked trans-membrane domain m2 proton channel from influenza a virus.
Authors: Hu, J. / Asbury, T. / Achuthan, S. / Li, C. / Bertram, R. / Quine, J.R. / Fu, R. / Cross, T.A.
History
DepositionJun 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2


Theoretical massNumber of molelcules
Total (without water)7,8344
Polymers7,8344
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 / 72structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide
Matrix protein 2


Mass: 1958.496 Da / Num. of mol.: 4 / Fragment: TRANSMEMBRANE DOMAIN (RESIDUES 26-43) / Source method: obtained synthetically
Details: THE PEPTIDE WAS SYNTHESIZED USING SOLID PHASE PEPTIDE SYNTHESIS. THIS SEQUENCE OCCURS NATURALLY IN THE INFLUENZA A VIRUS (UDORN/72).
References: UniProt: P35938, UniProt: Q3LZC0*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentType: solid-State NMR PISEMA

-
Sample preparation

DetailsContents: M2-TMD (~120 mg) and DMPC (~75 mg) were first co-dissolved in 10 ml TFE, followed by the removal of the solvent under vacuum. The peptide/lipid mixture was rehydrated and sonicated to make ...Contents: M2-TMD (~120 mg) and DMPC (~75 mg) were first co-dissolved in 10 ml TFE, followed by the removal of the solvent under vacuum. The peptide/lipid mixture was rehydrated and sonicated to make liposomes in a citrate-borate-phosphate (CBP) buffer (pH 8.8) with 1 mM EDTA and 10 mM amantadine at 310 K. The liposomes were pelleted by ultracentrifugation . Then the pellet was spread on glass slides and dehydrated in a 75% humidity chamber. The dehydrated slides were rehydrated with 1.5 microl liter CBP buffer per slide followed by being stacked into a glass tube and incubated at 316 K for 24 hours in 96% relative humidity. Finally, the glass tube was sealed at both ends with epoxy and two glasscaps.
Solvent system: oriented peptide/lipid bilayer of M2_TMD and DMPC
Sample conditionspH: 8.8 / Pressure: AMBIENT / Temperature: 308 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

-
Processing

NMR softwareName: XPLOR-NIH / Version: 2.9.9 / Developer: Schwieters, Kuszewski, Tjandra, Clore / Classification: refinement
RefinementMethod: ENERGY MINIMIZATION WITH ORIENTATIONAL CONSTRAINTS / Software ordinal: 1
Details: REFINEMENT WAS CARRIED OUT IN VACUO ON INITIAL MONOMER COORDINATES CONSISTING OF TWO ALPHA-HELICAL FRAGMENTS (3.6 RESIDUES PER TURN) HAVING TILT AND ROTATIONAL ORIENTATIONS WITH RESPECT TO ...Details: REFINEMENT WAS CARRIED OUT IN VACUO ON INITIAL MONOMER COORDINATES CONSISTING OF TWO ALPHA-HELICAL FRAGMENTS (3.6 RESIDUES PER TURN) HAVING TILT AND ROTATIONAL ORIENTATIONS WITH RESPECT TO THE BILAYER DERIVED FROM PISEMA DIPOLAR WAVE ANALYSIS. ENERGY MINIMIZATION USED A GLOBAL PENALTY FUNCTION INCORPORATING ORIENTATIONAL RESTRAINTS, HYDROGEN BONDING AND THE CHARMM EMPIRICAL FUNCTION. THE ORIENTATIONAL RESTRAINTS IMPOSED ON THE STRUCTURE DURING REFINEMENT ARE 16 15N CHEMICAL SHIFTS AND 16 15N-1H DIPOLAR COUPLINGS FROM PISEMA EXPERIMENTS. A SYMMETRIC, TETRAMERIC BUNDLE MODEL OF M2-TMD WAS CONSTRUCTED BY A SERIES OF RIGID-BODY TRANSFORMATIONS OF THE REFINED M2-TMD MONOMER. THE RESULTING HOMO-TETRAMER IS THE LOWEST FREE ENERGY CONFORMER BASED ON ROTATIONAL CONFORMATIONAL SEARCH. NOTE THAT THE HIS37 AND TRP41 SIDECHAIN POSITIONS ARE CONSISTENT WITH MEASURED ORIENTATIONAL CONSTRAINTS. THE ROTAMERIC STATES OF OTHER RESIDUES ARE TAKEN FROM A BACKBONE DEPENDENT SIDECHAIN ROTAMER LIBRARY (SCRWL).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 72 / 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://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