[English] 日本語
Yorodumi
- PDB-7mgx: Structure of EmrE-D3 mutant in complex with monobody L10 and meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mgx
TitleStructure of EmrE-D3 mutant in complex with monobody L10 and methyl viologen
Components
  • L10 Monobody
  • Multidrug transporter EmrE
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / small multidrug resistance transporter / paraquat / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / glycine betaine transport / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / response to osmotic stress / xenobiotic transport / transmembrane transporter activity ...EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / glycine betaine transport / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / response to osmotic stress / xenobiotic transport / transmembrane transporter activity / xenobiotic transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane
Similarity search - Function
Small drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein
Similarity search - Domain/homology
1,1'-dimethyl-4,4'-bipyridin-1-ium / Multidrug transporter EmrE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsKermani, A.A. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1845012 United States
CitationJournal: Elife / Year: 2022
Title: Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates.
Authors: Kermani, A.A. / Burata, O.E. / Koff, B.B. / Koide, A. / Koide, S. / Stockbridge, R.B.
History
DepositionApr 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Multidrug transporter EmrE
C: L10 Monobody
E: Multidrug transporter EmrE
G: L10 Monobody
B: Multidrug transporter EmrE
D: L10 Monobody
F: Multidrug transporter EmrE
H: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,72910
Polymers87,3578
Non-polymers3732
Water00
1
A: Multidrug transporter EmrE
C: L10 Monobody
B: Multidrug transporter EmrE
D: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8655
Polymers43,6784
Non-polymers1861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Multidrug transporter EmrE
G: L10 Monobody
F: Multidrug transporter EmrE
H: L10 Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8655
Polymers43,6784
Non-polymers1861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.910, 75.070, 111.430
Angle α, β, γ (deg.)92.030, 90.330, 109.200
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Multidrug transporter EmrE / Efflux-multidrug resistance protein EmrE / Ethidium resistance protein / Methyl viologen resistance protein C


Mass: 11907.279 Da / Num. of mol.: 4 / Mutation: E25N, W31I, V34M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: emrE, eb, mvrC, b0543, JW0531 / Production host: Escherichia coli (E. coli) / References: UniProt: P23895
#2: Antibody
L10 Monobody


Mass: 9931.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-KHJ / 1,1'-dimethyl-4,4'-bipyridin-1-ium


Mass: 186.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NH4SO4, 0.1 M ADA, pH 6.3, 35% PEG600

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.13→70.839 Å / Num. obs: 14289 / % possible obs: 82 % / Redundancy: 3.7 % / CC1/2: 0.939 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.1 / Net I/σ(I): 7.7
Reflection shellResolution: 3.13→3.419 Å / Num. unique obs: 714 / CC1/2: 0.629 / % possible all: 72.3

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MH6

7mh6


Resolution: 3.13→32.92 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 46.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3317 700 4.93 %
Rwork0.3059 13496 -
obs0.3071 14263 51.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.19 Å2 / Biso mean: 74.0881 Å2 / Biso min: 36.01 Å2
Refinement stepCycle: final / Resolution: 3.13→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 28 0 5836
Biso mean--76.21 --
Num. residues----760
LS refinement shellResolution: 3.13→3.24 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.574 28 -
Rwork0.3873 --
obs--10 %

+
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