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- EMDB-63854: Cryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion ch... -

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Basic information

Entry
Database: EMDB / ID: EMD-63854
TitleCryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion chromatography peak1
Map dataCryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion chromatography peak1
Sample
  • Complex: Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusion chromatography peak1
    • Protein or peptide: MmpL4 protein
    • Protein or peptide: Meromycolate extension acyl carrier protein
KeywordsEfflux pump MSMEG_3496-AcpM complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / 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
MmpL4 protein / Meromycolate extension acyl carrier protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsGao F / Zhang X / Li D / Ma X
Funding support China, 2 items
OrganizationGrant numberCountry
Other government202403021211192 China
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_63854.png

Downloads & links

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Map

FileDownload / File: emd_63854.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion chromatography peak1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.3712176 - 0.8862986
Average (Standard dev.)-0.0007410297 (±0.018221863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of MSMEG 3496 in complex with AcpM,...

Fileemd_63854_half_map_1.map
AnnotationCryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion chromatography peak1,half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of MSMEG 3496 in complex with AcpM,...

Fileemd_63854_half_map_2.map
AnnotationCryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion chromatography peak1,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 : Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusi...

EntireName: Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusion chromatography peak1
Components
  • Complex: Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusion chromatography peak1
    • Protein or peptide: MmpL4 protein
    • Protein or peptide: Meromycolate extension acyl carrier protein

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Supramolecule #1: Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusi...

SupramoleculeName: Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusion chromatography peak1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: MmpL4 protein

MacromoleculeName: MmpL4 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 110.357641 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSNPSHDAPT DAMGVSGPKH ARPGGIAKWI RVLAVPIILV WVAIIAVLNT VVPQLDVVGE MRSVSMSPDD APSVIAMKRV GEVFEEFKS NSSVMIVLEG EQPLGDEAHK YYDEIVDKLE ADPAHVEHVQ DFWGDPLTAS GAQSPDGLAS YVQVYTRGNQ G EALANESV ...String:
MSNPSHDAPT DAMGVSGPKH ARPGGIAKWI RVLAVPIILV WVAIIAVLNT VVPQLDVVGE MRSVSMSPDD APSVIAMKRV GEVFEEFKS NSSVMIVLEG EQPLGDEAHK YYDEIVDKLE ADPAHVEHVQ DFWGDPLTAS GAQSPDGLAS YVQVYTRGNQ G EALANESV EAVQDIVESV PAPPGVKAYV TGPAALSADQ HVASDRSVRV IEALTFAVII TMLLLVYRSI VTVILTLVMV VL SLSAARG MIAFLGYHEI IGLSVFATNL LTTLAIAAAT DYAIFLIGRY QEARSVGEDR EQSYYTMFHS TAHVVLGSGM TIA GATLCL HFTRMPYFQS LGIPLAIGMS VVVLASLTMG AAIISVASRF GKTFEPKRAM RTRGWRKLGA AVVRWPAPIL VTTI ALSVV GLLALPGYQT NYNDRRYLPQ DLPANTGYAA ADRHFSQARM NPELLMIESD HDLRNSADFL VVDRIAKRVF QVPGI SRVQ AITRPQGTPI EHTSIPFQIS MSGTTQMMNM KYMQDRMADM LVMADEMQKS VDTMEEMLKI TREMSDTTHS MVGKMH GMV EDIKELRDHI ADFDDFLRPI RNYFYWEPHC DSIPVCQSIR SIFDTLDGID VMTDDIQRLM PDMDRLDELM PQMLTIM PP MIESMKTMKT MMLTTQATMG GLQDQMEAAM ENQTAMGQAF DASKNDDSFY LPPETFENPD FKRGMKMFLS PDGHAVRF I ISHEGDPMSP EGIKHIDAIK QAAKEAIKGT PLEGSKIYLG GTAATFKDLQ EGANYDLIIA GIAALCLIFI IMLIITRAV VASAVIVGTV VISLGASFGL SVLIWQHIIG LELHWMVLAM AVIVLLAVGA DYNLLLVSRI KEEIHAGLNT GIIRSMGGTG SVVTSAGLV FAFTMMSMAV SELAVIAQVG TTIGLGLLFD TLVIRSFMTP SIAALMGKWF WWPQRVRQRP LPAPWPQPVQ R DPEDALNR VAAAENLYFQ GLWSHPQFEK GGGSGGGSGG SAWSHPQFEK

UniProtKB: MmpL4 protein

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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

Concentration5.28 mg/mL
BufferpH: 8
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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4926409
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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