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- EMDB-32538: Cryo-EM structure of Mycobacterium tuberculosis irtAB complexed w... -

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Basic information

Entry
Database: EMDB / ID: EMD-32538
TitleCryo-EM structure of Mycobacterium tuberculosis irtAB complexed with ATP in an occluded conformation
Map data
Sample
  • Complex: IrtAB
    • Protein or peptide: Mycobactin import ATP-binding/permease protein IrtB
    • Protein or peptide: Mycobactin import ATP-binding/permease protein IrtA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsIrtAB / ABC exporter-liker importer / Iron-loaded siderophore / Mycobacterium tuberculosis / MEMBRANE PROTEIN
Function / homology
Function and homology information


iron acquisition from host / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / Mtb iron assimilation by chelation / cellular response to iron ion starvation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / FAD binding / intracellular iron ion homeostasis ...iron acquisition from host / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / Mtb iron assimilation by chelation / cellular response to iron ion starvation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / FAD binding / intracellular iron ion homeostasis / oxidoreductase activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / 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 / FAD-binding domain, ferredoxin reductase-type ...Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / 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 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / 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
Mycobactin import ATP-binding/permease protein IrtB / Mycobactin import ATP-binding/permease protein IrtA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsZhang B / Sun S
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)81772204 China
National Natural Science Foundation of China (NSFC)32171217 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
CitationJournal: Protein Cell / Year: 2023
Title: Cryo-EM structures for the Mycobacterium tuberculosis iron-loaded siderophore transporter IrtAB.
Authors: Shan Sun / Yan Gao / Xiaolin Yang / Xiuna Yang / Tianyu Hu / Jingxi Liang / Zhiqi Xiong / Yuting Ran / Pengxuan Ren / Fang Bai / Luke W Guddat / Haitao Yang / Zihe Rao / Bing Zhang /
Abstract: The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import ...The adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, IrtAB, plays a vital role in the replication and viability of Mycobacterium tuberculosis (Mtb), where its function is to import iron-loaded siderophores. Unusually, it adopts the canonical type IV exporter fold. Herein, we report the structure of unliganded Mtb IrtAB and its structure in complex with ATP, ADP, or ATP analogue (AMP-PNP) at resolutions ranging from 2.8 to 3.5 Å. The structure of IrtAB bound ATP-Mg2+ shows a "head-to-tail" dimer of nucleotide-binding domains (NBDs), a closed amphipathic cavity within the transmembrane domains (TMDs), and a metal ion liganded to three histidine residues of IrtA in the cavity. Cryo-electron microscopy (Cryo-EM) structures and ATP hydrolysis assays show that the NBD of IrtA has a higher affinity for nucleotides and increased ATPase activity compared with IrtB. Moreover, the metal ion located in the TM region of IrtA is critical for the stabilization of the conformation of IrtAB during the transport cycle. This study provides a structural basis to explain the ATP-driven conformational changes that occur in IrtAB.
History
DepositionJan 5, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32538.png

Downloads & links

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Map

FileDownload / File: emd_32538.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.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.1738434 - 2.8737025
Average (Standard dev.)-0.00008592208 (±0.05659972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : IrtAB

EntireName: IrtAB
Components
  • Complex: IrtAB
    • Protein or peptide: Mycobactin import ATP-binding/permease protein IrtB
    • Protein or peptide: Mycobactin import ATP-binding/permease protein IrtA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: IrtAB

SupramoleculeName: IrtAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

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Macromolecule #1: Mycobactin import ATP-binding/permease protein IrtB

MacromoleculeName: Mycobactin import ATP-binding/permease protein IrtB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 61.008051 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MIRTWIALVP NDHRARLIGF ALLAFCSVVA RAVGTVLLVP LMAALFGEAP QRAWLWLGWL SAATVAGWVL DAVTARIGIE LGFAVLNHT QHDVADRLPV VRLDWFTAEN TATARQAIAA TGPELVGLVV NLVTPLTSAI LLPAVIALAL LPISWQLGVA A LAGVPLLL ...String:
MIRTWIALVP NDHRARLIGF ALLAFCSVVA RAVGTVLLVP LMAALFGEAP QRAWLWLGWL SAATVAGWVL DAVTARIGIE LGFAVLNHT QHDVADRLPV VRLDWFTAEN TATARQAIAA TGPELVGLVV NLVTPLTSAI LLPAVIALAL LPISWQLGVA A LAGVPLLL GALWASAAFA RRADTAADKA NTALTERIIE FARTQQALRA ARRVEPARSL VGNALASQHT ATMRLLGMQI PG QLLFSIA SQLALIVLAG TTAALTITGT LTVPEAIALI VVMVRYLEPF TAVSELAPAL ESTRATLGRI GSVLTAPVMV AGS GTWRDG AVVPRIEFDD VAFGYDGGSG PVLDGVSFCL QPGTTTAIVG PSGCGKSTIL ALIAGLHQPT RGRVLIDGTD VATL DARAQ QAVCSVVFQH PYLFHGTIRD NVFAADPGAS DDQFAQAVRL ARVDELIARL PDGANTIVGE AGSALSGGER QRVSI ARAL LKAAPVLLVD QATSALDAEN EAAVVDALAA DPRSRTRVIV AHRLASIRHA DRVLFVDDGR VVEDGSISEL LTAGGR FSQ FWRQQHEAAE WQILAE

UniProtKB: Mycobactin import ATP-binding/permease protein IrtB

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Macromolecule #2: Mycobactin import ATP-binding/permease protein IrtA

MacromoleculeName: Mycobactin import ATP-binding/permease protein IrtA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 93.070758 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MARGLQGVML RSFGARDHTA TVIETISIAP HFVRVRMVSP TLFQDAEAEP AAWLRFWFPD PNGSNTEFQR AYTISEADPA AGRFAVDVV LHDPAGPASS WARTVKPGAT IAVMSLMGSS RFDVPEEQPA GYLLIGDSAS IPGMNGIIET VPNDVPIEMY L EQHDDNDT ...String:
MARGLQGVML RSFGARDHTA TVIETISIAP HFVRVRMVSP TLFQDAEAEP AAWLRFWFPD PNGSNTEFQR AYTISEADPA AGRFAVDVV LHDPAGPASS WARTVKPGAT IAVMSLMGSS RFDVPEEQPA GYLLIGDSAS IPGMNGIIET VPNDVPIEMY L EQHDDNDT LIPLAKHPRL RVRWVMRRDE KSLAEAIENR DWSDWYAWAT PEAAALKCVR VRLRDEFGFP KSEIHAQAYW NA GRAMGTH RATEPAATEP EVGAAPQPES AVPAPARGSW RAQAASRLLA PLKLPLVLSG VLAALVTLAQ LAPFVLLVEL SRL LVSGAG AHRLFTVGFA AVGLLGTGAL LAAALTLWLH VIDARFARAL RLRLLSKLSR LPLGWFTSRG SGSIKKLVTD DTLA LHYLV THAVPDAVAA VVAPVGVLVY LFVVDWRVAL VLFGPVLVYL TITSSLTIQS GPRIVQAQRW AEKMNGEAGS YLEGQ PVIR VFGAASSSFR RRLDEYIGFL VAWQRPLAGK KTLMDLATRP ATFLWLIAAT GTLLVATHRM DPVNLLPFMF LGTTFG ARL LGIAYGLGGL RTGLLAARHL QVTLDETELA VREHPREPLD GEAPATVVFD HVTFGYRPGV PVIQDVSLTL RPGTVTA LV GPSGSGKSTL ATLLARFHDV ERGAIRVGGQ DIRSLAADEL YTRVGFVLQE AQLVHGTAAE NIALAVPDAP AEQVQVAA R EAQIHDRVLR LPDGYDTVLG ANSGLSGGER QRLTIARAIL GDTPVLILDQ ATAFADPESE YLVQQALNRL TRDRTVLVI AHRLHTITRA DQIVVLDHGR IVERGTHEEL LAAGGRYCRL WDTGQGSRVA VAAAQDGTR

UniProtKB: Mycobactin import ATP-binding/permease protein IrtA

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 QUANTUM (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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101408
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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