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- EMDB-44435: Cryo-EM structure of a bacterial prototype ATP-binding cassette t... -

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Basic information

Entry
Database: EMDB / ID: EMD-44435
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 transport system permease protein MalF
    • Protein or peptide: Maltose/maltodextrin transport system permease protein MalG
    • Protein or peptide: Maltose/maltodextrin import ATP-binding protein MalK
    • Protein or peptide: Maltose/maltodextrin import ATP-binding protein MalK
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: 3.26 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: To Be Published
Title: Engineering membrane scaffold peptides to enable detergent-free reconstitution of native NDs
Authors: 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
History
DepositionApr 9, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44435.png

Downloads & links

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Map

FileDownload / File: emd_44435.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å		1.06 Å/pix.
x 300 pix.
= 317.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.197
Minimum - Maximum-0.37385565 - 0.80590534
Average (Standard dev.)0.0007363363 (±0.016468989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44435_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_44435_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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 transport system permease protein MalF
    • Protein or peptide: Maltose/maltodextrin transport system permease protein MalG
    • Protein or peptide: Maltose/maltodextrin import ATP-binding protein MalK
    • Protein or peptide: Maltose/maltodextrin import ATP-binding protein MalK

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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: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Maltose/maltodextrin transport system permease protein MalF

MacromoleculeName: Maltose/maltodextrin transport system permease protein MalF
type: protein_or_peptide / ID: 1 / 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 #2: Maltose/maltodextrin transport system permease protein MalG

MacromoleculeName: Maltose/maltodextrin transport system permease protein MalG
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 31.53134 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AMVQPKSQKA RLFITHLLLL LFIAAIMFPL LMVVAISLRQ GNFATGSLWP EQISWDHWKL ALGFSVEQAD GRIWPPPFPV LLWLWNSVK VAGISAIGIV ALSTTCAYAF ARMRFPGKAT LLKGMLIFQM FPAVLSLVAL YALFDRLGEY IPFIGLNTHG G VIFAYLGG ...String:
AMVQPKSQKA RLFITHLLLL LFIAAIMFPL LMVVAISLRQ GNFATGSLWP EQISWDHWKL ALGFSVEQAD GRIWPPPFPV LLWLWNSVK VAGISAIGIV ALSTTCAYAF ARMRFPGKAT LLKGMLIFQM FPAVLSLVAL YALFDRLGEY IPFIGLNTHG G VIFAYLGG IALHVWTIKG YFETIDSSLE EAAALDGATP WQAFRLVLLP LSVPILAVVF ILSFIAAITE VPVASLLLRD VN SYTLAVG MQQYLNPQNY LWGDFAAAAV MSALPITIVF LLAQRWLVN

UniProtKB: Maltose/maltodextrin transport system permease protein MalG

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Macromolecule #3: Maltose/maltodextrin import ATP-binding protein MalK

MacromoleculeName: Maltose/maltodextrin import ATP-binding protein MalK / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: Maltose/maltodextrin import ATP-binding protein MalK

MacromoleculeName: Maltose/maltodextrin import ATP-binding protein MalK / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type maltose transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 41.255527 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 EPGVAHH

UniProtKB: Maltose/maltodextrin import ATP-binding protein MalK

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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: 1.116 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7t4e

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 452428
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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