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- EMDB-21600: Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21600 | |||||||||||||||||||||
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Title | Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria, Mutant R1389S Class 1 | |||||||||||||||||||||
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Function / homology | Alpha-(1->3)-arabinofuranosyltransferase / Alpha-(1->3)-arabinofuranosyltransferase / Coagulation factors 5/8 type C domain (FA58C) profile. / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / transferase activity / membrane => GO:0016020 / DUF3367 domain-containing protein![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
![]() | Tan YZ / Zhang L / Rodrigues J / Zheng RB / Giacometti SI / Rosario AL / Kloss B / Dandey VP / Wei H / Brunton R ...Tan YZ / Zhang L / Rodrigues J / Zheng RB / Giacometti SI / Rosario AL / Kloss B / Dandey VP / Wei H / Brunton R / Raczkowski AM / Athayde D / Catalao MJ / Pimentel M / Clarke OB / Lowary TL / Archer M / Niederweis M / Potter CS / Carragher B / Mancia F | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Authors: Yong Zi Tan / Lei Zhang / José Rodrigues / Ruixiang Blake Zheng / Sabrina I Giacometti / Ana L Rosário / Brian Kloss / Venkata P Dandey / Hui Wei / Richard Brunton / Ashleigh M Raczkowski ...Authors: Yong Zi Tan / Lei Zhang / José Rodrigues / Ruixiang Blake Zheng / Sabrina I Giacometti / Ana L Rosário / Brian Kloss / Venkata P Dandey / Hui Wei / Richard Brunton / Ashleigh M Raczkowski / Diogo Athayde / Maria João Catalão / Madalena Pimentel / Oliver B Clarke / Todd L Lowary / Margarida Archer / Michael Niederweis / Clinton S Potter / Bridget Carragher / Filippo Mancia / ![]() ![]() ![]() ![]() Abstract: Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two ...Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function. | |||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 56.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 33.1 KB 33.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.8 KB | Display | ![]() |
Images | ![]() | 495.9 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 16.8 MB 8 MB 6.8 MB 105.9 KB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wbxMC ![]() 6w98C ![]() 6wbyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 2.3 TB Data #1: Unaligned and compressed multi-frame movies [micrographs - multiframe] Data #2: Aligned and dose-weighted micrographs [micrographs - single frame] Data #3: Final Particle Stacks with Refined Euler Angles and Shifts (Overall and Focused Refined on CBM3) [picked particles - single frame - processed]) |
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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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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: Raw map
File | emd_21600_additional_1.map | ||||||||||||
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Annotation | Raw map | ||||||||||||
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-Additional map: 3DFSC
File | emd_21600_additional_2.map | ||||||||||||
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Annotation | 3DFSC | ||||||||||||
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-Additional map: 3DFSC - Thresholded
File | emd_21600_additional_3.map | ||||||||||||
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Annotation | 3DFSC - Thresholded | ||||||||||||
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-Additional map: 3DFSC - Thresholded, Binarized
File | emd_21600_additional_4.map | ||||||||||||
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Annotation | 3DFSC - Thresholded, Binarized | ||||||||||||
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-Half map: Half map 1
File | emd_21600_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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-Half map: Half map 2
File | emd_21600_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Sample components
-Entire : Mutant R1389S Class 1 Mycobacterial Arabinofuranosyltransferase A...
Entire | Name: Mutant R1389S Class 1 Mycobacterial Arabinofuranosyltransferase AftD Complexed with Acyl Carrier Protein |
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Components |
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-Supramolecule #1: Mutant R1389S Class 1 Mycobacterial Arabinofuranosyltransferase A...
Supramolecule | Name: Mutant R1389S Class 1 Mycobacterial Arabinofuranosyltransferase AftD Complexed with Acyl Carrier Protein type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 5 MDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: DUF3367 domain-containing protein
Macromolecule | Name: DUF3367 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 152.818641 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDYKDDDDKH HHHHHHHHHE NLYFQSYVMT YRLDSSALSR RWLAVAAAVS LLLTFSQSPG QISPDTKLDL AINPLRFAAR ALNLWSSDL PFGQAQNQAY GYLFPHGAFF SLGHLLGVPA WVTQRLWWAL LIVAGFWGLI RVAEALGIGT RGSRIIAAVA F ALSPRVLT ...String: MDYKDDDDKH HHHHHHHHHE NLYFQSYVMT YRLDSSALSR RWLAVAAAVS LLLTFSQSPG QISPDTKLDL AINPLRFAAR ALNLWSSDL PFGQAQNQAY GYLFPHGAFF SLGHLLGVPA WVTQRLWWAL LIVAGFWGLI RVAEALGIGT RGSRIIAAVA F ALSPRVLT TLGAISSETL PMMLAPWVLL PLILTFQGRM SPRRAAALSA VAVALMGAVN AVATALACGV AVIWWLAHRP NR TWWRFTA WWIPCLALAS TWWIVALLIF GKISPKFLDF IESSGVTTQW TSLTEVLRGT DSWTPFVAPT ATAGSSLVTQ SAM VIATTM LAAAGMAGLA MRGMPARGRL VAVLLIGLVL LTAGYTGALG SPIAQQIQFF LDDGGTPLRN VHKLEPLIRL PLIL GLAHA LSRIPLPASV PVRQWLSALA RPERNRAVAF AIVLLVALAA STSLAWTGRL VPRGGFDAIP GYWNDTAHWL ADHDT GGRA LVVPGAPFAI QTWGLTRDEP LQALGQTPWG VRDSIPLTPP ETIRAIDSVQ QLFAAGRPSD GLADTLREQG ISYLVV RND LDPDTSRSAR PILVHHTIEG SPGLTKVAQF GDPVGAGAVE GFVADSDLRP QYPAVEIYAV GANDHDGEPY FTDIDTM PR VAGGPEALLR LNERRRQLNE PPLGPSLLAT DAAQAGLRPG PAVVTDTPLA RETDYGRVDD HSSAIRAPGD KRRTFNRV P DYPATGVPLV NGSWTGGTIT ASSSASDSTA LPNVAPGTST AAAIDRDNAT SWVSSSLEAA LGQWIRIDLD RPITNAILT VTPSATALGA QVRRLEVETD NGTTSVRFDE PGQPLNIALR PGETTWVKVT ATGTDDGTSG VQFGVTELSL TQYDAAGFAH TVDLRHSAT VPPPPAGDNP LGWDLGSPLQ GRSGCAPSPQ RLRCAATLSL APEEPGTFIR TLTVPQPVSL TPRLWVRARP G PQLRDLIQ QPGTTVATGD SDVIDPQGSS YAATDGDPGT VWTAPQDSVQ RLHLPSLVIK LPKPTAIGAI RLRPSRTEVP AH PKQVAIN LGDGPQLRSI DPKADVTELA LHPSITDTIT VTVTDWTDII DRTALGFDQL KPPGIAEVIA LDADHRPIAP ADN AANSKR KITIGCNRGP ILALAGRFVP MSITATVREL LDGTVIQATP CDTSPIATGA GIQDVTVNPS QQFIVDGVQL TAAA TEPAS ATMTVAPKGA WGPDRREVTA EPSAHERVLA VPESINPGWA ARDAQGHLLT PVRVNGWQQG WVLPAGDGGK ITLTF GLNT WYRAGLFGGL ALLPILACLA LLPARGRTTL PPVAPWCAGP AAGVAVLAAL TAISGISGMA VGLAALAFKV WTRWPL RAV TAAGVYLAGG SLLLAGAALS RHPWRSVGGY TGHSWWIQLL ALISVASVAL AAVSLPSRRC WKRRSASREG DSTSA |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: Solution was filtered and degassed. | |||||||||
Grid | Model: UltrAuFoil / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 298 K / Instrument: LEICA EM GP | |||||||||
Details | Protein was incorporated into lipid nanodiscs. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-90 / Number grids imaged: 1 / Number real images: 4886 / Average exposure time: 13.05 sec. / Average electron dose: 96.78 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |