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- EMDB-49659: Cryo-EM structure of a bacterial prototype ATP-binding cassette t... -

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Basic information

Entry
Database: EMDB / ID: EMD-49659
TitleCryo-EM structure of a bacterial prototype ATP-binding cassette transporter MalFGK2.
Map data
Sample
  • Complex: ATP-binding cassette transporter MalFGK2
    • Protein or peptide: Maltose/maltodextrin import ATP-binding protein MalK
    • Protein or peptide: Maltose/maltodextrin transport system permease protein MalF
    • Protein or peptide: Maltose/maltodextrin transport system permease protein MalG
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION
Keywordsbacterial prototype ATP-binding cassette transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / maltose transport complex / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / DNA-binding transcription factor binding / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / : ...Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / : / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsQian R / Jing W / Vinay I / Shanwen Z / Jeehae S / William GL / Luis MRH / Jong HS / Young AG / IIya L ...Qian R / Jing W / Vinay I / Shanwen Z / Jeehae S / William GL / Luis MRH / Jong HS / Young AG / IIya L / Kirill M / Baron C / Huan B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM140920 United States
CitationJournal: Nat Commun / Year: 2025
Title: DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides.
Authors: Qian Ren / Jing Wang / Vinay Idikuda / Shanwen Zhang / Jeehae Shin / W Grant Ludlam / Luis M Real Hernandez / Sara Zdancewicz / Alex J B Kreutzberger / Hucheng Chang / Volker Kiessling / ...Authors: Qian Ren / Jing Wang / Vinay Idikuda / Shanwen Zhang / Jeehae Shin / W Grant Ludlam / Luis M Real Hernandez / Sara Zdancewicz / Alex J B Kreutzberger / Hucheng Chang / Volker Kiessling / Lukas K Tamm / Ahmad Jomaa / Ilya Levental / Kirill Martemyanov / Baron Chanda / Huan Bao /
Abstract: Membrane scaffold protein-based nanodiscs have facilitated unprecedented structural and biophysical analysis of membrane proteins in a near-native lipid environment. However, successful ...Membrane scaffold protein-based nanodiscs have facilitated unprecedented structural and biophysical analysis of membrane proteins in a near-native lipid environment. However, successful reconstitution of membrane proteins in nanodiscs requires prior solubilization and purification in detergents, which may impact their physiological structure and function. Furthermore, the detergent-mediated reconstitution of nanodiscs is unlikely to recapitulate the precise composition or asymmetry of native membranes. To circumvent this fundamental limitation of traditional nanodisc technology, we herein describe the development of membrane-solubilizing peptides to directly extract membrane proteins from native cell membranes into nanoscale discoids. By systematically protein engineering and screening, we create a class of chemically modified Apolipoprotein-A1 mimetic peptides to enable the formation of detergent-free nanodiscs with high efficiency. Nanodiscs generated with these engineered membrane scaffold peptides are suitable for obtaining high-resolution structures using single-particle cryo-EM with native lipids. To further highlight the versatility of our approach, we directly extract a sampling of membrane signaling proteins with their surrounding native membranes for biochemical and biophysical interrogations.
History
DepositionMar 12, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49659.png

Downloads & links

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Map

FileDownload / File: emd_49659.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.32 Å		0.83 Å/pix.
x 320 pix.
= 264.32 Å		0.83 Å/pix.
x 320 pix.
= 264.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.21528547 - 0.45798445
Average (Standard dev.)0.0010475696 (±0.0128582865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49659_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49659_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : ATP-binding cassette transporter MalFGK2

EntireName: ATP-binding cassette transporter MalFGK2
Components
  • Complex: ATP-binding cassette transporter MalFGK2
    • Protein or peptide: Maltose/maltodextrin import ATP-binding protein MalK
    • Protein or peptide: Maltose/maltodextrin transport system permease protein MalF
    • Protein or peptide: Maltose/maltodextrin transport system permease protein MalG
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: VANADATE ION

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Supramolecule #1: ATP-binding cassette transporter MalFGK2

SupramoleculeName: ATP-binding cassette transporter MalFGK2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Maltose/maltodextrin import ATP-binding protein MalK

MacromoleculeName: Maltose/maltodextrin import ATP-binding protein MalK / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type maltose transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 40.979234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ASVQLQNVTK AWGEVVVSKD INLDIHEGEF VVFVGPSGCG KSTLLRMIAG LETITSGDLF IGEKRMNDTP PAERGVGMVF QSYALYPHL SVAENMSFGL KLAGAKKEVI NQRVNQVAEV LQLAHLLDRK PKALSGGQRQ RVAIGRTLVA EPSVFLLDEP L SNLDAALR ...String:
ASVQLQNVTK AWGEVVVSKD INLDIHEGEF VVFVGPSGCG KSTLLRMIAG LETITSGDLF IGEKRMNDTP PAERGVGMVF QSYALYPHL SVAENMSFGL KLAGAKKEVI NQRVNQVAEV LQLAHLLDRK PKALSGGQRQ RVAIGRTLVA EPSVFLLDEP L SNLDAALR VQMRIEISRL HKRLGRTMIY VTHDQVEAMT LADKIVVLDA GRVAQVGKPL ELYHYPADRF VAGFIGSPKM NF LPVKVTA TAIDQVQVEL PMPNRQQVWL PVESRDVQVG ANMSLGIRPE HLLPSDIADV ILEGEVQVVE QLGNETQIHI QIP SIRQNL VYRQNDVVLV EEGATFAIGL PPERCHLFRE DGTACRRLHK EPGVA

UniProtKB: Maltose/maltodextrin import ATP-binding protein MalK

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Macromolecule #2: Maltose/maltodextrin transport system permease protein MalF

MacromoleculeName: Maltose/maltodextrin transport system permease protein MalF
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 57.052898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDVIKKKHWW QSDALKWSVL GLLGLLVGYL VVLMYAQGEY LFAITTLILS SAGLYIFANR KAYAWRYVYP GMAGMGLFVL FPLVCTIAI AFTNYSSTNQ LTFERAQEVL LDRSWQAGKT YNFGLYPAGD EWQLALSDGE TGKNYLSDAF KFGGEQKLQL K ETTAQPEG ...String:
MDVIKKKHWW QSDALKWSVL GLLGLLVGYL VVLMYAQGEY LFAITTLILS SAGLYIFANR KAYAWRYVYP GMAGMGLFVL FPLVCTIAI AFTNYSSTNQ LTFERAQEVL LDRSWQAGKT YNFGLYPAGD EWQLALSDGE TGKNYLSDAF KFGGEQKLQL K ETTAQPEG ERANLRVITQ NRQALSDITA ILPDGNKVMM SSLRQFSGTQ PLYTLDGDGT LTNNQSGVKY RPNNQIGFYQ SI TADGNWG DEKLSPGYTV TTGWKNFTRV FTDEGIQKPF LAIFVWTVVF SLITVFLTVA VGMVLACLVQ WEALRGKAVY RVL LILPYA VPSFISILIF KGLFNQSFGE INMMLSALFG VKPAWFSDPT TARTMLIIVN TWLGYPYMMI LCMGLLKAIP DDLY EASAM DGAGPFQNFF KITLPLLIKP LTPLMIASFA FNFNNFVLIQ LLTNGGPDRL GTTTPAGYTD LLVNYTYRIA FEGGG GQDF GLAAAIATLI FLLVGALAIV NLKATRMKFD

UniProtKB: Maltose/maltodextrin transport system permease protein MalF

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Macromolecule #3: Maltose/maltodextrin transport system permease protein MalG

MacromoleculeName: Maltose/maltodextrin transport system permease protein MalG
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 32.246227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMVQPKSQK ARLFITHLLL LLFIAAIMFP LLMVVAISLR QGNFATGSLI PEQISWDHWK LALGFSVEQA DGRITPPPFP VLLWLWNSV KVAGISAIGI VALSTTCAYA FARMRFPGKA TLLKGMLIFQ MFPAVLSLVA LYALFDRLGE YIPFIGLNTH G GVIFAYLG ...String:
MAMVQPKSQK ARLFITHLLL LLFIAAIMFP LLMVVAISLR QGNFATGSLI PEQISWDHWK LALGFSVEQA DGRITPPPFP VLLWLWNSV KVAGISAIGI VALSTTCAYA FARMRFPGKA TLLKGMLIFQ MFPAVLSLVA LYALFDRLGE YIPFIGLNTH G GVIFAYLG GIALHVWTIK GYFETIDSSL EEAAALDGAT PWQAFRLVLL PLSVPILAVV FILSFIAAIT EVPVASLLLR DV NSYTLAV GMQQYLNPQN YLWGDFAAAA VMSALPITIV FLLAQRWLVN GLTAGGVKG

UniProtKB: Maltose/maltodextrin transport system permease protein MalG

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #6: VANADATE ION

MacromoleculeName: VANADATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: VO4
Molecular weightTheoretical: 114.939 Da
Chemical component information

ChemComp-VN3:
VANADATE ION

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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

Concentration2 mg/mL
BufferpH: 8
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.172 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3rlf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125454
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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