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- EMDB-30216: Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferas... -

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Basic information

Entry
Database: EMDB / ID: EMD-30216
TitleCryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol
Map data
Sample
  • Complex: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol
    • Complex: EmbA-EmbB
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
    • Complex: AcpM
      • Protein or peptide: Meromycolate extension acyl carrier protein
  • Ligand: CARDIOLIPIN
  • Ligand: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
  • Ligand: CALCIUM ION
  • Ligand: 4'-PHOSPHOPANTETHEINE
  • Ligand: PHOSPHATE ION
  • Ligand: Ethambutol
Function / homology
Function and homology information


indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / Transferases; Glycosyltransferases; Pentosyltransferases / acyl carrier activity / cell wall organization / plasma membrane / cytoplasm
Similarity search - Function
: / Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / Acyl carrier protein (ACP) ...: / Arabinofuranosyltransferase, central domain / Arabinofuranosyltransferase, domain 1 / Arabinosyltransferase, C-terminal / Arabinosyltransferas, concanavalin like domain / Arabinosyltransferase, C-terminal, subdomain 2 / Mycobacterial cell wall arabinan synthesis protein / EmbC C-terminal domain / Arabinosyltransferase concanavalin like domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Meromycolate extension acyl carrier protein / Probable arabinosyltransferase B / Probable arabinosyltransferase A / Integral membrane indolylacetylinositol arabinosyltransferase EmbB
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang L / Zhao Y / Gao Y / Wang Q / Li J / Besra GS / Rao Z
Funding support China, United Kingdom, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29020000 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
National Natural Science Foundation of China (NSFC)81520108019 China
Medical Research Council (MRC, United Kingdom)MR/S000542/1 United Kingdom
CitationJournal: Science / Year: 2020
Title: Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol.
Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang ...Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang / Manfu Wang / Yan Zhu / Bing Zhang / Lijun Bi / Xian'en Zhang / Haitao Yang / Luke W Guddat / Wenqing Xu / Quan Wang / Jun Li / Gurdyal S Besra / Zihe Rao /
Abstract: The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo- ...The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents.
History
DepositionApr 10, 2020-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7bvc
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30216.png

Downloads & links

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Map

FileDownload / File: emd_30216.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: 0.25 / Movie #1: 0.28
Minimum - Maximum-1.6482817 - 3.0549002
Average (Standard dev.)-0.0002157968 (±0.06968946)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.6483.055-0.000

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Supplemental data

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Mask #1

Fileemd_30216_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30216_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30216_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in ...

EntireName: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol
Components
  • Complex: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol
    • Complex: EmbA-EmbB
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
      • Protein or peptide: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
    • Complex: AcpM
      • Protein or peptide: Meromycolate extension acyl carrier protein
  • Ligand: CARDIOLIPIN
  • Ligand: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
  • Ligand: CALCIUM ION
  • Ligand: 4'-PHOSPHOPANTETHEINE
  • Ligand: PHOSPHATE ION
  • Ligand: Ethambutol

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Supramolecule #1: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in ...

SupramoleculeName: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: EmbA-EmbB

SupramoleculeName: EmbA-EmbB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Supramolecule #3: AcpM

SupramoleculeName: AcpM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Integral membrane indolylacetylinositol arabinosyltransferase EmbA

MacromoleculeName: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Pentosyltransferases
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 116.561898 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: DYKDDDDKMT EPSRIARLIA VVAGIAGVLL CGLVPLLPVE ETTATVLWPQ GVGADGNVTE LTAPLVAGAP RALDVTIPCR AVAELPADG GVVFSTNPAG GIEAGRNGMF IRANADVVYV AFRDTVAAVA PREAVDSGAC SEIHVWADVS AVGADFAGIP D ASGTLPVD ...String:
DYKDDDDKMT EPSRIARLIA VVAGIAGVLL CGLVPLLPVE ETTATVLWPQ GVGADGNVTE LTAPLVAGAP RALDVTIPCR AVAELPADG GVVFSTNPAG GIEAGRNGMF IRANADVVYV AFRDTVAAVA PREAVDSGAC SEIHVWADVS AVGADFAGIP D ASGTLPVD KRPQVSGVFT DLKVPAQPGL AARIDIDTRF ITSPTLLKTA VMVLGLACVI GSIVALALLD RGWRRRPPRT RG RAGLWTW ITDTGVIGGL LIWHIVGAPT SDDGYNMTIA RVASEAGYTT NYYRYFGASE APFDWYQSVL SHLASISTAG VWM RLPATA AAIATWLIIS RCVLPRIGRR VAANRVAMLT AGATFLAAWL PFNNGLRPEP LIAFAVITVW MLVENSIGTR RLWP AAVAI VIAMFSVTLA PQGLIALAPL LVGARAIGRV VTARRAGTGI LASLAPLAAS VAVVFVIIFR DQTLATVAES VRIKY VVGP TIPWYQEFLR YYFLTVEDSV DGSLTRRFAV LVLLLCLFGL IMVLLRRGRV PGAVSGPLWR LCGSTAIGLL LLILTP TKW AIQFGAFAGL AGALGGVTAF AFARVGLHSR RNLALYVTAL LFILAWATSG LNGWFYVGNY GVPWFDKQPV IAHYPVT TI FLVLAIVGGL LAGWLHFRMD YAGHTEVADT GRNRALASTP LLIVATIMVV LELGSMVKAT VGRYPVYTVG SANIAALR S AGDSCAMADA VLVEADPNEG MLQPVPGQRF GEYGPLGGED PVGFTPNGVS DTLEPAEPVA ANPGTPNSDG PVDKPNIGI GYAAGTGGGY GPEGVNGSRV FLPFGLDPSR TPVMGSYGEN KLAAKATSAW YQLPPRTPDR PLVTVAAAGA IWYYEEDGSF NYGQSLKLQ WGVHRPDGTY QALSEVQPID IFQQKAWRNL RFPLAWAPPE ANVARIVADD PNLSEDQWFA FTPPRVPVLQ T AQQFLGSQ TPVLMDIATA ANFPCQRPFA ERLGVAELPE YRIIPNFKQM VVSSNQWQSA ADGGPFLFIQ ALLRTEAIPT YL RDDWYRD WGSIERYIRV VPQEQAPTAA IEEGSTRVFG WSRGGPIRAL P

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Macromolecule #2: Integral membrane indolylacetylinositol arabinosyltransferase EmbB

MacromoleculeName: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: indolylacetylinositol arabinosyltransferase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 119.077672 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSGNMDEAVS GNMDEAVSAG KDVRIARWVA TIAGLLGFVL SVSIPLLPVT QTTATLNWPQ QGRLDNVTAP LISQAPLELT ATVPCSVVR DLPPEGGLVF GTAPAEGRDA ALNAMLVNVT ETRVDVIVRN VVVASVNRDR VAGPDCQRIE ITSNLDGTYA D FVGLTQIS ...String:
MSGNMDEAVS GNMDEAVSAG KDVRIARWVA TIAGLLGFVL SVSIPLLPVT QTTATLNWPQ QGRLDNVTAP LISQAPLELT ATVPCSVVR DLPPEGGLVF GTAPAEGRDA ALNAMLVNVT ETRVDVIVRN VVVASVNRDR VAGPDCQRIE ITSNLDGTYA D FVGLTQIS GEDAGKLQRT GYPDPNLRPA IVGVFTDLTG PAPQGLSVSA EIDTRFTTHP TALKLAAMLL AIVSTVIALL AL WRLDRLD GRRMHRLIPT RWRTVTAVDG VVVGGMAIWY VIGANSSDDG YILQMARTAE HAGYMANYFR WFGSPEDPFG WYY NVLALM TKVSDASIWI RLPDLICALI CWLLLSREVL PRLGPAVAGS RAAMWAAGLV LLGAWMPFNN GLRPEGQIAT GALI TYVLI ERAVTSGRLT PAALAITTAA FTLGIQPTGL IAVAALLAGG RPILRIVMRR RRLVGTWPLI APLLAAGTVI LAVVF ADQT IATVLEATRI RTAIGPSQEW WTENLRYYYL ILPTTDGAIS RRVAFVFTAM CLFPSLFMML RRKHIAGVAR GPAWRL MGI IFATMFFLMF TPTKWIHHFG LFAAVGGAMA ALATVLVSPT VLRSARNRMA FLSLVLFVLA FCFASTNGWW YVSNFGA PF NNSVPKVGGV QISAIFFALS AIAALWAFWL HLTRRTESRV VDRLTAAPIP VAAGFMVVVM MASMAIGVVR QYPTYSNG W ANIRAFAGGC GLADDVLVEP DSNAGFLTPL PGAYGPLGPL GGEDPQGFSP DGVPDRIIAE AIRLNNPQPG TDYDWNRPI KLDEPGINGS TVPLPYGLDP KRVPVAGTYS TEAQQESRLS SAWYELPARD ETERAAHPLV VITAAGTITG ESVANGLTTG QTVDLEYAT RGPDGTLVPA GRVTPYDVGP TPSWRNLRYP RSEIPDDAVA VRVVAEDLSL SQGDWIAVTP PRVPELQSVQ E YVGSDQPV LMDWAVGLAF PCQQPMLHAN GVTEVPKFRI SPDYYAKLQS TDTWQDGING GLLGITDLLL RASVMSTYLS QD WGQDWGS LRKFDTVVEA TPAELDFGSQ THSGLYSPGP LRIRPHLGGI KAFHHHHHHH HHH

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Macromolecule #3: Meromycolate extension acyl carrier protein

MacromoleculeName: Meromycolate extension acyl carrier protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 10.743876 KDa
SequenceString:
MAATQEEIIA GLAEIIEEVT GIEPSEVTPE KSFVDDLDID SLSMVEIAVQ TEDKYGVKIP DEDLAGLRTV GDVVAYIQKL EEENPEAAA ALREKFAADQ

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Macromolecule #4: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 4 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #5: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decameth...

MacromoleculeName: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate
type: ligand / ID: 5 / Number of copies: 1 / Formula: F8L
Molecular weightTheoretical: 911.28 Da
Chemical component information

ChemComp-F8L:
[(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE

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Macromolecule #8: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #9: Ethambutol

MacromoleculeName: Ethambutol / type: ligand / ID: 9 / Number of copies: 1 / Formula: 95E
Molecular weightTheoretical: 204.31 Da
Chemical component information

ChemComp-95E:
Ethambutol / medication*YM

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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

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
20.0 mMHepes
150.0 mMNaCl
0.04 w/vGDN
GridModel: Quantifoil R0.6/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE
DetailsThe sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.5 K / Max: 78.6 K
Alignment procedureComa free - Residual tilt: 10.0 mrad
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 5100 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / 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: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were normalized.
Particle selectionNumber selected: 1855947
CTF correctionSoftware - Name: cryoSPARC (ver. 2.9.1)
Details: The CTF correction was done by patch CTF correction.
Startup modelType of model: NONE / Details: The startup models were generated automatically.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 227206
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9.1)
Details: The initial angle assignment was generated by Ab-initio reconstruction.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9.1)
Details: The final angle assignment was non-uniform refinement.
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 2.9.1)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Overall B value: 62.01 / Target criteria: correlation coefficient
Output model

PDB-7bvc:
Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol

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