[English] 日本語
Yorodumi
- EMDB-38628: Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38628
TitleCryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ADP-bound IFasym-3 state (ADP 4 degrees C treated)
Map data
Sample
  • Complex: MsRv1273c/72c,MSMEG_5008-MSMEG_5009
    • Protein or peptide: Transmembrane ATP-binding protein ABC transporter
    • Protein or peptide: ABC transporter transmembrane region
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsABC Transporter / exporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphate-transporting ATPase / ABC-type oligopeptide transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transmembrane ATP-binding protein ABC transporter / ABC transporter transmembrane region
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYu J / Li J
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1300900 China
Ministry of Science and Technology (MoST, China)2022YFC230900 China
Other government22ZR1441600
CitationJournal: Nat Commun / Year: 2025
Title: Structure and mechanism of a mycobacterial isoniazid efflux pump MsRv1273c/72c with a degenerate nucleotide-binding site.
Authors: Jing Yu / Yuhui Lan / Chen Zhu / Zhendong Chen / Junyi Pan / Yanfeng Shi / Lan Yang / Tianyu Hu / Yan Gao / Yao Zhao / Xiaobo Chen / Xiuna Yang / Shuihua Lu / Luke W Guddat / Haitao Yang / Zihe Rao / Jun Li /
Abstract: Heterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. ...Heterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. However, the structural basis of their transport mechanism remains to be explained. Here, we determine mycobacterial MsRv1273c/72c to be an isoniazid efflux pump and determine several structures by cryo-electron microscopy showing specific asymmetrical features including an N-terminal extending loop and a periplasmic helical hairpin only found in MsRv1272c. In addition, we capture three distinct asymmetric states where the nucleotide-binding domains are partially dimerized at the degenerate site. Using these intermediate states, the D-WalkerB loop and X-signature loop of MsRv1272c modulate and couple the function of both NBSs through conformational changes. Thus, these data provide insights into the mechanism of this heterodimeric ABC transporter containing a degenerate NBS. The structures also provide a framework for the rational design of anti-tuberculosis drugs targeting this drug-efflux pump.
History
DepositionJan 9, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38628.png

Downloads & links

-
Map

FileDownload / File: emd_38628.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 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: 0.22
Minimum - Maximum-2.020179 - 3.4099543
Average (Standard dev.)-0.0006316996 (±0.08043755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38628_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38628_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MsRv1273c/72c,MSMEG_5008-MSMEG_5009

EntireName: MsRv1273c/72c,MSMEG_5008-MSMEG_5009
Components
  • Complex: MsRv1273c/72c,MSMEG_5008-MSMEG_5009
    • Protein or peptide: Transmembrane ATP-binding protein ABC transporter
    • Protein or peptide: ABC transporter transmembrane region
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: MsRv1273c/72c,MSMEG_5008-MSMEG_5009

SupramoleculeName: MsRv1273c/72c,MSMEG_5008-MSMEG_5009 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

-
Macromolecule #1: Transmembrane ATP-binding protein ABC transporter

MacromoleculeName: Transmembrane ATP-binding protein ABC transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 63.010496 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: SYFQSNMLWA LLRQYVRPYR WLLAVVAVLQ VISNMASLYL PTVNAAIIDD GVAKGDTARI VELGAVMLGV TALQVVCAVG AVFFGARAA TGFGHDLRAA VFTHVTTFSA EEAGRFGAAS LLTRTTNDVG HIQQLVQLTV TMLITAPIMS IGGIFMALHQ D AGLSWLLL ...String:
SYFQSNMLWA LLRQYVRPYR WLLAVVAVLQ VISNMASLYL PTVNAAIIDD GVAKGDTARI VELGAVMLGV TALQVVCAVG AVFFGARAA TGFGHDLRAA VFTHVTTFSA EEAGRFGAAS LLTRTTNDVG HIQQLVQLTV TMLITAPIMS IGGIFMALHQ D AGLSWLLL VSVPVLGLAN YWIIRHLMPV FTRMQSLIDG INRVLRDQLS GIRVIRAFAR EPLERVRFAE ANQTLSDSAL EA GRWQALM LPVTTLVINV SSVALIWFGG LRIDAGQMQV GSLIAFLAYF MQILMAVLMA TFMLVIFPRA AVCADRIGEV LST QTAITN PADPVRPAAI AGDIGVHDAT FCYPGADRPV LQDVSFTVPR GTTTAVVGST GSGKSTLISL ICRLYDVTSG SLRI DGVDV RDLDIEQLWS AIGLVPQRGY LFSGTVAENL RYGRADATDD EMWEALRVAA AADFVRAHPQ GLDMPVAQGG INFSG GQRQ RLAIARAVIR RPAIYLFDDA FSALDVHTDA RVRDALREVA ADATVVIVSQ RISTVIEADQ VVVIDDGRVV GIGTHD TLL ADCPIYAEFA ESQALTAGEP R

UniProtKB: Transmembrane ATP-binding protein ABC transporter

-
Macromolecule #2: ABC transporter transmembrane region

MacromoleculeName: ABC transporter transmembrane region / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 70.310273 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MRRGALPQAP LERTRDFKGS AIRLARRLLP QRALTLAVIL LGVGGIAIGV IGPRILGHAT DLLFNGVIGR ELPAGLTKEQ AVEAARARG DGTFADLLSG MDIVPGQGVD FGAVGRTLAL ALGLYLVAAL LVWVQARLLN VTVQRTMVAL RAEVQEKIHR L PLSYFDSR ...String:
MRRGALPQAP LERTRDFKGS AIRLARRLLP QRALTLAVIL LGVGGIAIGV IGPRILGHAT DLLFNGVIGR ELPAGLTKEQ AVEAARARG DGTFADLLSG MDIVPGQGVD FGAVGRTLAL ALGLYLVAAL LVWVQARLLN VTVQRTMVAL RAEVQEKIHR L PLSYFDSR QRGEVLSRVT NDVDNIQNSV SMTISQLLTS VLTVFAVLVM MLTISPLLTL FTVVTVPASL WVTRWITRRS QP LFVAQWR NTGRLAAHLE ETYSGFTIVK TFGHREAAAG KFAELNSETQ QSSFGAQFFS GLVSPATMFI GNLSYVAVAV VGG LQVATG QITLGSIQAF IQYVRQFNQP LTQVAGMYNT LQSGIASAER VFDLLDTEEE SADSPRRADV RTGRVEFEHV SFSY VPGTP VIEDLSLVAE PGSTVAIVGP TGAGKTTLVN LLMRFYDVDS GRITIDGVDI ASVSRESLRA SIGMVLQDTW LFAGT IYDN IAYGRPDADE DEVIEAATAA YVDRFVHTLP NGYDTRVDDD GGAISAGEKQ LITIARAVLA RPKLLVLDEA TSSVDT RTE LLIAHAMAEL RRDRTSFIIA HRLSTIRDAD LILVMDSGRI IERGTHEELL ARHGRYWEMT RVHLGGIKAF HHHHHHH HH H

UniProtKB: ABC transporter transmembrane region

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155852
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