[English] 日本語
Yorodumi
- EMDB-44594: BRD-8000.3 bound EFPA transporter of Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44594
TitleBRD-8000.3 bound EFPA transporter of Mycobacterium tuberculosis
Map dataSharp map after focused refinement in cryosparc.
Sample
  • Complex: EfpA
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide
  • Ligand: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordstransporter / MEMBRANE PROTEIN
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / transmembrane transporter activity / MFS transporter superfamily / membrane / plasma membrane / Uncharacterized MFS-type transporter EfpA
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsKhandelwal NK / Gupta M / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485 United States
CitationJournal: To Be Published
Title: Inhibitor BRD-8000.3 bound EfpA transporter of Mycobacterium tuberculosis
Authors: Khandelwal NK / Gupta M / Stroud RM
History
DepositionApr 23, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44594.png

Downloads & links

-
Map

FileDownload / File: emd_44594.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map after focused refinement in cryosparc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 440 pix.
= 367.4 Å		0.84 Å/pix.
x 440 pix.
= 367.4 Å		0.84 Å/pix.
x 440 pix.
= 367.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.4980166 - 2.8855488
Average (Standard dev.)0.001016284 (±0.05335054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 367.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_44594_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened map after focused refinement in cryosparc.

Fileemd_44594_additional_1.map
Annotationunsharpened map after focused refinement in cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A from focused refinement in cryosparc

Fileemd_44594_half_map_1.map
AnnotationHalf map A from focused refinement in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B from focused refinement in cryosparc

Fileemd_44594_half_map_2.map
AnnotationHalf map B from focused refinement in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EfpA

EntireName: EfpA
Components
  • Complex: EfpA
    • Protein or peptide: Uncharacterized MFS-type transporter EfpA
  • Ligand: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide
  • Ligand: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: EfpA

SupramoleculeName: EfpA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 66.53956 KDa

-
Macromolecule #1: Uncharacterized MFS-type transporter EfpA

MacromoleculeName: Uncharacterized MFS-type transporter EfpA / type: protein_or_peptide / ID: 1
Details: Amino acid 1-4 start codon and GSSG linker, Amnio acid 5- 12 Flag tag, Amnio acid 13-15 SGS linker, Amino acid 16-21 thrombin site, Amino acid 22-128 BRIL-Tag, Amino acid 129-610 ...Details: Amino acid 1-4 start codon and GSSG linker, Amnio acid 5- 12 Flag tag, Amnio acid 13-15 SGS linker, Amino acid 16-21 thrombin site, Amino acid 22-128 BRIL-Tag, Amino acid 129-610 Mycobacterium tuberculosis EfpA (truncated from 48 N terminal amino acid) with mutation of Proline at position 171 to Arginine, Amino acid 611-612 SS linker, Amino acid 613-619 TEV site, Amino acid 620-629 10XHis.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 66.602242 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSDYKDDD DKSSGLVPRG SMADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLR SFIAAVIAIG GMQLLATMDS TVAIVALPKI Q NELSLSDA ...String:
MGSSDYKDDD DKSSGLVPRG SMADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLR SFIAAVIAIG GMQLLATMDS TVAIVALPKI Q NELSLSDA GRSWVITAYV LTFGGLMLLG GRLGDTIGRK RTFIVGVALF TISSVLCAVA WDEATLVIAR LSQGVGSAIA SP TGLALVA TTFRKGPARN AATAVFAAMT AIGSVMGLVV GGALTEVSWR WAFLVNVPIG LVMIYLARTA LRETNKERMK LDA TGAILA TLACTAAVFA FSIGPEKGWM SGITIGSGLV ALAAAVAFVI VERTAENPVV PFHLFRDRNR LVTFSAILLA GGVM FSLTV CIGLYVQDIL GYSALRAGVG FIPFVIAMGI GLGVSSQLVS RFSPRVLTIG GGYLLFGAML YGSFFMHRGV PYFPN LVMP IVVGGIGIGM AVVPLTLSAI AGVGFDQIGP VSAIALMLQS LGGPLVLAVI QAVITSRTLY LGGTTGPVKF MNDVQL AAL DHAYTYGLLW VAGAAIIVGG MALFIGYTPQ QVAHAQEVKE AIDAGELSSE NLYFQGHHHH HHHHHH

UniProtKB: Uncharacterized MFS-type transporter EfpA

-
Macromolecule #2: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3...

MacromoleculeName: (1S,3S)-N-[6-bromo-5-(pyrimidin-2-yl)pyridin-2-yl]-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropane-1-carboxamide
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1AQR
Molecular weightTheoretical: 401.3 Da

-
Macromolecule #3: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphory...

MacromoleculeName: [(2~{R})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] octadecanoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1H2V
Molecular weightTheoretical: 751.023 Da

-
Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.91 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chloride
50.0 mMTrisTris

Details: 50mM Tris-HCL, 300 mM NaCL, 0.02% GDN, 0.002 %CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.033 kPa / Details: 30 sec glow 30 sec hold at 15mA.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsProtein incubated with BRD-8000.3 100 micro molar final concentration on ice for 15 and used for grid preparation.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10235 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5484905
CTF correctionSoftware - Name: cryoSPARC (ver. v4.2.1) / Type: NONE
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1) / Number images used: 121230
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.2.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9bin:
BRD-8000.3 bound EFPA transporter of Mycobacterium tuberculosis

+
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