[English] 日本語
Yorodumi
- PDB-9syv: Symmetric hexameric MmpS4-MmpL4 complex from Mycobacterium tuberc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9syv
TitleSymmetric hexameric MmpS4-MmpL4 complex from Mycobacterium tuberculosis
Components
  • Siderophore export accessory protein MmpS4
  • Siderophore exporter MmpL4
KeywordsMEMBRANE PROTEIN / RND superfamily / MmpL family / siderophore export / drug resistance
Function / homology
Function and homology information


peptidoglycan-based cell wall / extracellular region / plasma membrane
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
Similarity search - Domain/homology
Siderophore export accessory protein MmpS4 / Siderophore exporter MmpL4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsLichti, N.P. / Earp, J.C. / Garaeva, A.A. / Seeger, M.A.
Funding supportEuropean Union, Switzerland, United States, Germany, 5items
OrganizationGrant numberCountry
European Research Council (ERC)772190European Union
University of ZurichFK-21-041 Switzerland
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 Al151239 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 Al137338 United States
Boehringer Ingelheim Fonds (BIF)NA Germany
CitationJournal: bioRxiv / Year: 2026
Title: Structural elucidation of the hexameric MmpS4-MmpL4 complex from .
Authors: Jennifer C Earp / Nicolas P Lichti / Alisa A Garaeva / Virginia Meikle / Michael Niederweis / Markus A Seeger /
Abstract: contains thirteen Mycobacterial membrane protein Large (MmpL) transporters, which belong to the family of secondary active RND transporters. MmpL4 and MmpL5, together with their operon partners ... contains thirteen Mycobacterial membrane protein Large (MmpL) transporters, which belong to the family of secondary active RND transporters. MmpL4 and MmpL5, together with their operon partners MmpS4 and MmpS5, export the mycobacterial siderophore mycobactin and the last resort TB drug bedaquiline. Recently, we determined a structure of the MmpL4 monomer in complex with desferrated mycobactin, which lacked a functionally essential coiled-coil domain predicted to extend far into the periplasm. Here, we present a cryo-EM structure of the hexameric (MmpS4)-(MmpL4) complex, which was enabled by rational disulfide cross-links based on AlphaFold predictions. We observed density for the coiled-coil domain, which protrudes into the periplasmic space at an angle of around 60° relative to the symmetry axis of the MmpL4 trimer. In the context of the hexameric complex, MmpL4's conformation differs strikingly from the one observed for monomeric MmpL4, which includes formation of a large cavity in the periplasmic domain and rearrangements of conserved proton coupling residues at the transmembrane domain. Our work provides an experimental workflow to obtain single particle cryo-EM structures of labile multiprotein complexes by AlphaFold-informed stabilization of predicted protein interfaces.
History
DepositionOct 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Siderophore exporter MmpL4
B: Siderophore exporter MmpL4
C: Siderophore exporter MmpL4
D: Siderophore export accessory protein MmpS4
E: Siderophore export accessory protein MmpS4
F: Siderophore export accessory protein MmpS4


Theoretical massNumber of molelcules
Total (without water)362,4326
Polymers362,4326
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Siderophore exporter MmpL4


Mass: 105317.070 Da / Num. of mol.: 3 / Mutation: C39S, C319S, C335S, C393S, S434C, C780S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mmpL4, Rv0450c, MTV037.14c / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P9WJV3
#2: Protein Siderophore export accessory protein MmpS4 / PGB14T-X


Mass: 15493.614 Da / Num. of mol.: 3 / Mutation: D39C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mmpS4, Rv0451c, MTV037.15c / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P9WJS9
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Symmetric hexameric MmpS4-MmpL4 complex from Mycobacterium tuberculosisCOMPLEXall0RECOMBINANT
2MmpL4COMPLEX#11RECOMBINANTCysteine-depleted (C39S, C319S, C335S, C393S, C780S) full-length MmpL4 with S434C mutation
3MmpS4COMPLEX#21RECOMBINANTFull-length MmpS4 with D39C mutation
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.364 MDaNO
210.106 MDaNO
310.015 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mycobacterium tuberculosis (bacteria)1773
32Mycobacterium tuberculosis (bacteria)1773
43Mycobacterium tuberculosis (bacteria)1773
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli MC1061 (bacteria)1211845
32Escherichia coli MC1061 (bacteria)1211845
43Escherichia coli MC1061 (bacteria)1211845
Buffer solutionpH: 7.5 / Details: 20mM Tris-HC1 pH 7.5, 150mM NaC1, 0.03% DDM
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: at 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 62.92 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14584
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.7.0particle selection
2EPU2.9image acquisition
4cryoSPARC4.7.0CTF correction
7UCSF ChimeraXmodel fitting1.3
8Cootmodel fitting0.9.8.92
10cryoSPARC4.7.0initial Euler assignment
11cryoSPARC4.7.0final Euler assignment
12cryoSPARC4.7.0classification
13cryoSPARC4.7.03D reconstruction
14PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9066275
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76903 / Symmetry type: POINT
Atomic model buildingB value: 78.2 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 9GI0

9gi0


Accession code: 9GI0 / Chain residue range: 1-783 / Details: entire monomer used / Pdb chain residue range: 1-783 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417550
ELECTRON MICROSCOPYf_angle_d0.67923865
ELECTRON MICROSCOPYf_dihedral_angle_d3.9192442
ELECTRON MICROSCOPYf_chiral_restr0.0412853
ELECTRON MICROSCOPYf_plane_restr0.0062982

+
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