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- EMDB-32539: Cryo-EM structure of Mycobacterium tuberculosis irtAB in complex ... -
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Basic information
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Title | Cryo-EM structure of Mycobacterium tuberculosis irtAB in complex with ADP | |||||||||||||||
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![]() | IrtAB / ABC exporter-liker importer / Iron-loaded siderophore / Mycobacterium tuberculosis / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||||||||
![]() | Zhang B / Sun S | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 204.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
Images | ![]() | 111.2 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wixMC ![]() 7wiuC ![]() 7wivC ![]() 7wiwC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : IrtAB
Entire | Name: IrtAB |
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Components |
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-Supramolecule #1: IrtAB
Supramolecule | Name: IrtAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Mycobactin import ATP-binding/permease protein IrtA
Macromolecule | Name: Mycobactin import ATP-binding/permease protein IrtA / 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.07175 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 GDTPVLILDE ATAFADPESE YLVQQALNRL TRDRTVLVI AHRLHTITRA DQIVVLDHGR IVERGTHEEL LAAGGRYCRL WDTGQGSRVA VAAAQDGTR UniProtKB: Mycobactin import ATP-binding/permease protein IrtA |
-Macromolecule #2: Mycobactin import ATP-binding/permease protein IrtB
Macromolecule | Name: Mycobactin import ATP-binding/permease protein IrtB / 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 61.009035 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 EATSALDAEN EAAVVDALAA DPRSRTRVIV AHRLASIRHA DRVLFVDDGR VVEDGSISEL LTAGGR FSQ FWRQQHEAAE WQILAE UniProtKB: Mycobactin import ATP-binding/permease protein IrtB |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44951 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |