[English] 日本語
Yorodumi
- PDB-6us9: Influenza A M2 proton channel wild type TM domain bound to R-rima... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6us9
TitleInfluenza A M2 proton channel wild type TM domain bound to R-rimantadine
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / proton channel / rimantadine
Function / homology
Function and homology information


proton transmembrane transporter activity / host cell membrane / : / protein complex oligomerization / monoatomic ion channel activity / virion membrane / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
RIMANTADINE / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThomaston, J.L. / DeGrado, W.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM122603 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM117593 United States
CitationJournal: Biochemistry / Year: 2021
Title: Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity.
Authors: Thomaston, J.L. / Samways, M.L. / Konstantinidi, A. / Ma, C. / Hu, Y. / Bruce Macdonald, H.E. / Wang, J. / Essex, J.W. / DeGrado, W.F. / Kolocouris, A.
History
DepositionOct 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
I: Matrix protein 2
J: Matrix protein 2
K: Matrix protein 2
L: Matrix protein 2
M: Matrix protein 2
N: Matrix protein 2
O: Matrix protein 2
P: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,92824
Polymers44,06916
Non-polymers8598
Water90150
1
A: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2326
Polymers11,0174
Non-polymers2152
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-56 kcal/mol
Surface area5590 Å2
MethodPISA
2
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2326
Polymers11,0174
Non-polymers2152
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-53 kcal/mol
Surface area5740 Å2
MethodPISA
3
I: Matrix protein 2
J: Matrix protein 2
K: Matrix protein 2
L: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2326
Polymers11,0174
Non-polymers2152
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-53 kcal/mol
Surface area5520 Å2
MethodPISA
4
M: Matrix protein 2
N: Matrix protein 2
O: Matrix protein 2
P: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2326
Polymers11,0174
Non-polymers2152
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-54 kcal/mol
Surface area5480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.181, 48.701, 71.671
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein/peptide
Matrix protein 2


Mass: 2754.340 Da / Num. of mol.: 16 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/Jinfang/132/2002(H3N2))
References: UniProt: D5F6K1
#2: Chemical
ChemComp-RIM / RIMANTADINE / 1-(1-ADAMANTYL)ETHANAMINE / Rimantadine


Mass: 179.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.5
Details: monoolein, 0.015 M Tricine pH 8.5, 24% w/v PEG 4000, 50 mM MNG-3-C8, R-rimantadine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→48.7 Å / Num. obs: 21661 / % possible obs: 96 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.8024980126 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.056 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1558 / CC1/2: 0.95 / Rpim(I) all: 0.247

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BKL

6bkl


Resolution: 2→48.18 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2754 1758 8.17 %
Rwork0.2321 19767 -
obs0.2356 21525 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.9 Å2
Refinement stepCycle: LAST / Resolution: 2→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 56 50 3050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.05451224318293172
X-RAY DIFFRACTIONf_angle_d2.221682094374400
X-RAY DIFFRACTIONf_chiral_restr1.37307817192628
X-RAY DIFFRACTIONf_plane_restr0.0053503583424472
X-RAY DIFFRACTIONf_dihedral_angle_d14.99724013691024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.39851310.27481479X-RAY DIFFRACTION93.7682003494
2.0541-2.11450.3267483125251300.2407334220461526X-RAY DIFFRACTION94.0374787053
2.1145-2.18280.3208951405561360.2491823488771421X-RAY DIFFRACTION91.5882352941
2.1828-2.26080.2825424003181330.2352518249711513X-RAY DIFFRACTION95.475638051
2.2608-2.35130.3200066883151290.2460585691781530X-RAY DIFFRACTION95.6195965418
2.3513-2.45830.326763111490.2253815721161549X-RAY DIFFRACTION96.9178082192
2.4583-2.58790.2341621259591270.227861217941515X-RAY DIFFRACTION95.5762514552
2.5879-2.75010.2343270693761450.2155116949151512X-RAY DIFFRACTION94.3084803643
2.7501-2.96240.2594984802461330.2099534536631538X-RAY DIFFRACTION96.5895953757
2.9624-3.26040.2634203580011390.227741337961564X-RAY DIFFRACTION96.4326160815
3.2604-3.73210.2455924796171440.228725259481535X-RAY DIFFRACTION96.1626575029
3.7321-4.70140.25376624081370.2277134536571515X-RAY DIFFRACTION93.9169982945
4.7014-48.18059926620.2919459706011250.2416687351570X-RAY DIFFRACTION93.1830676196

+
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