[English] 日本語
Yorodumi
- EMDB-60202: Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Myco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60202
TitleCryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis (Map-2)
Map data
Sample
  • Complex: membrane complex
    • Protein or peptide: Siderophore exporter MmpL5
    • Protein or peptide: Siderophore export accessory protein MmpS5
    • Protein or peptide: Meromycolate extension acyl carrier protein
  • Ligand: CARDIOLIPIN
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
Keywordsmembrane transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Transport accessory protein MmpS / Transport accessory protein MmpS, C-terminal / Mycobacterium membrane protein / Membrane transport protein MmpL family / : / : / Membrane transport protein MMPL domain / MMPL family / Acyl carrier protein (ACP) / Phosphopantetheine attachment site ...Transport accessory protein MmpS / Transport accessory protein MmpS, C-terminal / Mycobacterium membrane protein / Membrane transport protein MmpL family / : / : / Membrane transport protein MMPL domain / MMPL family / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Meromycolate extension acyl carrier protein / Siderophore export accessory protein MmpS5 / Siderophore exporter MmpL5
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria) / Mycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsZhang B / Xiong Z / Rao Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
National Natural Science Foundation of China (NSFC)32394010 China
CitationJournal: To Be Published
Title: membrane transporter
Authors: Zhang B / Xiong Z / Rao Z
History
DepositionMay 17, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60202.png

Downloads & links

-
Map

FileDownload / File: emd_60202.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.252
Minimum - Maximum-1.9823035 - 2.9817889
Average (Standard dev.)-0.000074291944 (±0.08282927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60202_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60202_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : membrane complex

EntireName: membrane complex
Components
  • Complex: membrane complex
    • Protein or peptide: Siderophore exporter MmpL5
    • Protein or peptide: Siderophore export accessory protein MmpS5
    • Protein or peptide: Meromycolate extension acyl carrier protein
  • Ligand: CARDIOLIPIN
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide

-
Supramolecule #1: membrane complex

SupramoleculeName: membrane complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

-
Macromolecule #1: Siderophore exporter MmpL5

MacromoleculeName: Siderophore exporter MmpL5 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 104.874656 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MIVQRTAAPT GSVPPDRHAA RPFIPRMIRT FAVPIILGWL VTIAVLNVTV PQLETVGQIQ AVSMSPDAAP SMISMKHIGK VFEEGDSDS AAMIVLEGQR PLGDAAHAFY DQMIGRLQAD TTHVQSLQDF WGDPLTATGA QSSDGKAAYV QVKLAGNQGE S LANESVEA ...String:
MIVQRTAAPT GSVPPDRHAA RPFIPRMIRT FAVPIILGWL VTIAVLNVTV PQLETVGQIQ AVSMSPDAAP SMISMKHIGK VFEEGDSDS AAMIVLEGQR PLGDAAHAFY DQMIGRLQAD TTHVQSLQDF WGDPLTATGA QSSDGKAAYV QVKLAGNQGE S LANESVEA VKTIVERLAP PPGVKVYVTG SAALVADQQQ AGDRSLQVIE AVTFTVIIVM LLLVYRSIIT SAIMLTMVVL GL LATRGGV AFLGFHRIIG LSTFATNLLV VLAIAAATDY AIFLIGRYQE ARGLGQDRES AYYTMFGGTA HVVLGSGLTI AGA TFCLSF TRLPYFQTLG VPLAIGMVIV VAAALTLGPA IIAVTSRFGK LLEPKRMARV RGWRKVGAAI VRWPGPILVG AVAL ALVGL LTLPGYRTNY NDRNYLPADL PANEGYAAAE RHFSQARMNP EVLMVESDHD MRNSADFLVI NKIAKAIFAV EGISR VQAI TRPDGKPIEH TSIPFLISMQ GTSQKLTEKY NQDLTARMLE QVNDIQSNID QMERMHSLTQ QMADVTHEMV IQMTGM VVD VEELRNHIAD FDDFFRPIRS YFYWEKHCYD IPVCWSLRSV FDTLDGIDVM TEDINNLLPL MQRLDTLMPQ LTAMMPE MI QTMKSMKAQM LSMHSTQEGL QDQMAAMQED SAAMGEAFDA SRNDDSFYLP PEVFDNPDFQ RGLEQFLSPD GHAVRFII S HEGDPMSQAG IARIAKIKTA AKEAIKGTPL EGSAIYLGGT AAMFKDLSDG NTYDLMIAGI SALCLIFIIM LITTRSVVA AAVIVGTVVL SLGASFGLSV LIWQHILGIE LHWLVLAMAV IILLAVGADY NLLLVARLKE EIHAGINTGI IRAMGGSGSV VTAAGLVFA FTMMSFAVSE LTVMAQVGTT IGMGLLFDTL IVRSFMTPSI AALLGKWFWW PQVVRQRPIP QPWPSPASAR T FALV

UniProtKB: Siderophore exporter MmpL5

-
Macromolecule #2: Siderophore export accessory protein MmpS5

MacromoleculeName: Siderophore export accessory protein MmpS5 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 15.261456 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MIGTLKRAWI PLLILVVVAI AGFTVQRIRT FFGSEGILVT PKVFADDPEP FDPKVVEYEV SGSGSYVNIN YLDLDAKPQR IDGAALPWS LTLKTTAPSA APNILAQGDG TSITCRITVD GEVKDERTAT GVDALTYCFV KSA

UniProtKB: Siderophore export accessory protein MmpS5

-
Macromolecule #3: Meromycolate extension acyl carrier protein

MacromoleculeName: Meromycolate extension acyl carrier protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 10.743876 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MAATQEEIIA GLAEIIEEVT GIEPSEVTPE KSFVDDLDID SLSMVEIAVQ TEDKYGVKIP DEDLAGLRTV GDVVAYIQKL EEENPEAAA ALREKFAADQ

UniProtKB: Meromycolate extension acyl carrier protein

-
Macromolecule #4: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 4 / Number of copies: 6 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

-
Macromolecule #5: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 5 / Number of copies: 6 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

-
Macromolecule #6: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-...

MacromoleculeName: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
type: ligand / ID: 6 / Number of copies: 3 / Formula: PN7
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PN7:
N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83178
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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