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- EMDB-63860: Cryo-EM structure of Mycobacterium tuberculosis MmpL5 in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63860
TitleCryo-EM structure of Mycobacterium tuberculosis MmpL5 in complex with AcpM
Map dataCryo-EM map of Mycobacterium tuberculosis MmpL5 in complex with AcpM
Sample
  • Complex: Mycobacterium tuberculosis MmpL5 in complex with AcpM
    • Protein or peptide: Siderophore exporter MmpL5
    • Protein or peptide: Meromycolate extension acyl carrier protein
KeywordsMycobacterium tuberculosis efflux pump MmpL5 in complex with meromycolate extension acyl carrier protein AcpM / MEMBRANE PROTEIN
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Membrane transport protein MmpL family / : / : / Membrane transport protein MMPL domain / MMPL family / 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 / Siderophore exporter MmpL5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / Mycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsGao F / Zhang X / Li D / Ma X
Funding support China, 2 items
OrganizationGrant numberCountry
Other government202403021211192
National Natural Science Foundation of China (NSFC)32161133022 China
CitationJournal: Sci China Life Sci / Year: 2025
Title: Cryo-EM structures of mycobacteria MmpL5-AcpM complex.
Authors: Delin Li / Xiaokang Zhang / Kai Yuan / Xiaomin Ma / Yucheng Wang / Pu Han / Junqing Sun / Tianling Guo / Xuefei Pang / Kefang Liu / Yan Wu / Yingxia Liu / Shuguang Tan / Xu Zhang / Haixia ...Authors: Delin Li / Xiaokang Zhang / Kai Yuan / Xiaomin Ma / Yucheng Wang / Pu Han / Junqing Sun / Tianling Guo / Xuefei Pang / Kefang Liu / Yan Wu / Yingxia Liu / Shuguang Tan / Xu Zhang / Haixia Xiao / George Fu Gao / Feng Gao /
History
DepositionMar 20, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63860.png

Downloads & links

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Map

FileDownload / File: emd_63860.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Mycobacterium tuberculosis MmpL5 in complex with AcpM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 240 pix.
= 206.4 Å		0.86 Å/pix.
x 240 pix.
= 206.4 Å		0.86 Å/pix.
x 240 pix.
= 206.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.21083046 - 0.4588817
Average (Standard dev.)-0.000007758893 (±0.015920674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 206.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of Mycobacterium tuberculosis MmpL5 in complex...

Fileemd_63860_half_map_1.map
AnnotationCryo-EM map of Mycobacterium tuberculosis MmpL5 in complex with AcpM,half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of Mycobacterium tuberculosis MmpL5 in complex...

Fileemd_63860_half_map_2.map
AnnotationCryo-EM map of Mycobacterium tuberculosis MmpL5 in complex with AcpM,half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis MmpL5 in complex with AcpM

EntireName: Mycobacterium tuberculosis MmpL5 in complex with AcpM
Components
  • Complex: Mycobacterium tuberculosis MmpL5 in complex with AcpM
    • Protein or peptide: Siderophore exporter MmpL5
    • Protein or peptide: Meromycolate extension acyl carrier protein

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Supramolecule #1: Mycobacterium tuberculosis MmpL5 in complex with AcpM

SupramoleculeName: Mycobacterium tuberculosis MmpL5 in complex with AcpM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Macromolecule #1: Siderophore exporter MmpL5

MacromoleculeName: Siderophore exporter MmpL5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 108.926016 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MIVQRTAAPT GSVPPDRHAA RPFIPRMIRT FAVPIILGWL VTIAVLNVTV PQLETVGQIQ AVSMSPDAAP SMISMKHIGK VFEEGDSDS AAMIVLEGQR PLGDAAHAFY DQMIGRLQAD TTHVQSLQDF WGDPLTATGA QSSDGKAAYV QVKLAGNQGE S LANESVEA ...String:
MIVQRTAAPT GSVPPDRHAA RPFIPRMIRT FAVPIILGWL VTIAVLNVTV PQLETVGQIQ AVSMSPDAAP SMISMKHIGK VFEEGDSDS AAMIVLEGQR PLGDAAHAFY DQMIGRLQAD TTHVQSLQDF WGDPLTATGA QSSDGKAAYV QVKLAGNQGE S LANESVEA VKTIVERLAP PPGVKVYVTG SAALVADQQQ AGDRSLQVIE AVTFTVIIVM LLLVYRSIIT SAIMLTMVVL GL LATRGGV AFLGFHRIIG LSTFATNLLV VLAIAAATDY AIFLIGRYQE ARGLGQDRES AYYTMFGGTA HVVLGSGLTI AGA TFCLSF TRLPYFQTLG VPLAIGMVIV VAAALTLGPA IIAVTSRFGK LLEPKRMARV RGWRKVGAAI VRWPGPILVG AVAL ALVGL LTLPGYRTNY NDRNYLPADL PANEGYAAAE RHFSQARMNP EVLMVESDHD MRNSADFLVI NKIAKAIFAV EGISR VQAI TRPDGKPIEH TSIPFLISMQ GTSQKLTEKY NQDLTARMLE QVNDIQSNID QMERMHSLTQ QMADVTHEMV IQMTGM VVD VEELRNHIAD FDDFFRPIRS YFYWEKHCYD IPVCWSLRSV FDTLDGIDVM TEDINNLLPL MQRLDTLMPQ LTAMMPE MI QTMKSMKAQM LSMHSTQEGL QDQMAAMQED SAAMGEAFDA SRNDDSFYLP PEVFDNPDFQ RGLEQFLSPD GHAVRFII S HEGDPMSQAG IARIAKIKTA AKEAIKGTPL EGSAIYLGGT AAMFKDLSDG NTYDLMIAGI SALCLIFIIM LITTRSVVA AAVIVGTVVL SLGASFGLSV LIWQHILGIE LHWLVLAMAV IILLAVGADY NLLLVARLKE EIHAGINTGI IRAMGGSGSV VTAAGLVFA FTMMSFAVSE LTVMAQVGTT IGMGLLFDTL IVRSFMTPSI AALLGKWFWW PQVVRQRPIP QPWPSPASAR T FALVAAAE NLYFQGLWSH PQFEKGGGSG GGSGGSAWSH PQFEK

UniProtKB: Siderophore exporter MmpL5

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Macromolecule #2: Meromycolate extension acyl carrier protein

MacromoleculeName: Meromycolate extension acyl carrier protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 11.084209 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MAATQEEIIA GLAEIIEEVT GIEPSEVTPE KSFVDDLDID (4HH)LSMVEIAVQ TEDKYGVKIP DEDLAGLRTV GDVVAY IQK LEEENPEAAA ALREKFAADQ

UniProtKB: Meromycolate extension acyl carrier protein

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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

Concentration6.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio 3d by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1975401
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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