[English] 日本語
Yorodumi
- PDB-2kj1: cytoplasmic domain structure of BM2 proton channel from influenza... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kj1
Titlecytoplasmic domain structure of BM2 proton channel from influenza B virus
ComponentsBM2 protein
KeywordsTRANSPORT PROTEIN / BM2 / influenza B / cytoplasmic domain / coiled coil
Function / homology
Function and homology information


proton transmembrane transport / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #350 / Influenza B matrix protein 2 / Influenza B matrix protein 2 (BM2) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesInfluenza B virus
MethodSOLUTION NMR / simulated annealing
AuthorsWang, J. / Pielak, R. / McClintock, M. / Chou, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Solution structure and functional analysis of the influenza B proton channel.
Authors: Wang, J. / Pielak, R.M. / McClintock, M.A. / Chou, J.J.
History
DepositionMay 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BM2 protein
B: BM2 protein
C: BM2 protein
D: BM2 protein


Theoretical massNumber of molelcules
Total (without water)41,4804
Polymers41,4804
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein
BM2 protein


Mass: 10369.915 Da / Num. of mol.: 4 / Fragment: residues 43-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Gene: BM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WD75

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1433D HNCA
1533D HN(CA)CB
1633D HNCO
1762D 1H-13C HSQC
181J(NCgamma-aliphatic)
194J-scaled TROSY-HNCO
11053D (1H-13C-HMQC)-NOESY-(1H-15N-TROSY)
11153D (1H-13C-HMQC)-NOESY-(1H-13C-HSQC)

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] cytoplasmic domain of BM2, 150 mM LMPG, 25 mM sodium chloride, 25 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
20.8 mM [U-100% 13C; U-100% 15N] cytoplasmic domain of BM2, 150 mM [U-100% 2H] LMPG, 25 mM sodium chloride, 25 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
30.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] cytoplasmic domain of BM2, 150 mM LMPG, 25 mM sodium chloride, 25 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
40.5 mM [U-10% 13C] cytoplasmic domain of BM2, 150 mM potassium form of LMPG, 25 mM potassium chloride, 25 mM TRIS, 2.9 % dGpdG, 93% H2O/7% D2O93% H2O/7% D2O
50.8 mM [ILV_methyl_13C; U-100% 15N; U-80% 2H] cytoplasmic domain of BM2, 150 mM [U-100% 2H] LMPG, 25 mM sodium chloride, 25 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
60.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] cytoplasmic domain of BM2, 150 mM LMPG, 25 mM sodium chloride, 25 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMcytoplasmic domain of BM2[U-100% 15N]1
150 mMLMPG1
25 mMsodium chloride1
25 mMTRIS1
0.8 mMcytoplasmic domain of BM2[U-100% 13C; U-100% 15N]2
150 mMLMPG[U-100% 2H]2
25 mMsodium chloride2
25 mMTRIS2
0.8 mMcytoplasmic domain of BM2[U-100% 13C; U-100% 15N; U-80% 2H]3
150 mMLMPG3
25 mMsodium chloride3
25 mMTRIS3
0.5 mMcytoplasmic domain of BM2[U-10% 13C]4
150 mMpotassium form of LMPG4
25 mMpotassium chloride4
25 mMTRIS4
2.9 %dGpdG4
0.8 mMcytoplasmic domain of BM2[ILV_methyl_13C; U-100% 15N; U-80% 2H]5
150 mMLMPG[U-100% 2H]5
25 mMsodium chloride5
25 mMTRIS5
0.8 mMcytoplasmic domain of BM2[U-100% 13C; U-100% 15N; U-80% 2H]6
150 mMLMPG6
25 mMsodium chloride6
25 mMTRIS6
Sample conditionsIonic strength: 25 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE9003

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, C.D. et al.refinement
NMRPipeDelaglio, F. et al.processing
NMRDrawDelaglio, F. et al.data analysis
XwinNMRBruker Biospincollection
TALOSCornilescu, G. et al.chemical shift calculation
ProcheckNMRLaskowski, R. et al.structure solution
CARAKeller, R. et al.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using the program XPLOR-NIH (Schwieters et al., 2002). The secondary structure of the monomer was first calculated from random coil using intra-subunit NOEs, ...Details: Structures were calculated using the program XPLOR-NIH (Schwieters et al., 2002). The secondary structure of the monomer was first calculated from random coil using intra-subunit NOEs, backbone dihedral restraints derived from chemical shifts (TALOS) (Cornilescu et al., 1999), and side chain χ1 restraints. A total of 20 monomer structures were calculated using a standard high-temperature simulated annealing (SA) protocol in which the bath temperature was cooled from 1000 to 200 K. To obtain an initial set of tetramer structures, four copies of the lowest-energy monomer structure calculated above were used. The same SA run was performed in the presence of inter-subunit NOEs and all other intra-subunit restraints. For each experimental inter-subunit NOE between two adjacent subunits, four identical distance restraints were assigned respectively to all pairs of neighboring subunits to satisfy the condition of C4 rotational symmetry. During the annealing run, the bath was cooled from 1000 to 200 K with a temperature step of 20 K. A total of 100 tetramer structures were calculated. For BM2(1-33), 15 low energy structures were selected as the structural ensemble.
NMR constraintsHydrogen bond constraints total count: 336 / Protein chi angle constraints total count: 124 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 204 / Protein psi angle constraints total count: 196
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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