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- EMDB-39739: Cryo-EM structure of Escherichia coli DppBCDF complex bound to AMPPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-39739
TitleCryo-EM structure of Escherichia coli DppBCDF complex bound to AMPPNP
Map data
Sample
  • Complex: DppBCDF bound to AMPPNP
    • Protein or peptide: Dipeptide transport system permease protein DppB
    • Protein or peptide: Dipeptide transport system permease protein DppC
    • Protein or peptide: Dipeptide transport ATP-binding protein DppD
    • Protein or peptide: Dipeptide transport ATP-binding protein DppF
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsABC importer / Peptide transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type dipeptide transporter / dipeptide transport / heme transmembrane transporter activity / heme transmembrane transport / dipeptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / protein transport / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity ...ABC-type dipeptide transporter / dipeptide transport / heme transmembrane transporter activity / heme transmembrane transport / dipeptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to radiation / protein transport / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / : / Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region ...: / : / Oligopeptide transport permease C-like, N-terminal domain / N-terminal TM domain of oligopeptide transport permease C / ABC transporter type 1, GsiC-like, N-terminal domain / : / : / Binding-prot-dependent transport system membrane comp, N-term / Oligopeptide/dipeptide ABC transporter, C-terminal / Oligopeptide/dipeptide transporter, C-terminal region / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dipeptide transport ATP-binding protein DppD / Dipeptide transport system permease protein DppB / Dipeptide transport system permease protein DppC / Dipeptide transport ATP-binding protein DppF
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi P / Huang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: PLoS Biol / Year: 2025
Title: Structural characterization of the ABC transporter DppABCDF in Escherichia coli reveals insights into dipeptide acquisition.
Authors: Panpan Li / Manfeng Zhang / Yihua Huang /
Abstract: The prokaryote-specific ATP-binding cassette (ABC) peptide transporters are involved in various physiological processes and plays an important role in transporting naturally occurring antibiotics ...The prokaryote-specific ATP-binding cassette (ABC) peptide transporters are involved in various physiological processes and plays an important role in transporting naturally occurring antibiotics across the membrane to their intracellular targets. The dipeptide transporter DppABCDF in Gram-negative bacteria is composed of five distinct subunits, yet its assembly and underlying peptide import mechanism remain elusive. Here, we report the cryo-EM structures of the DppBCDF translocator from Escherichia coli in both its apo form and in complexes bound to nonhydrolyzable or slowly hydrolyzable ATP analogs (AMPPNP and ATPγS), as well as the ATPγS-bound DppABCDF full transporter. Unlike the reported heterotrimeric Mycobacterium tuberculosis DppBCD translocator, the E. coli DppBCDF translocator is a heterotetramer, with a [4Fe-4S] cluster at the C-terminus of each ATPase subunit. Structural studies reveal that ATPγS/AMPPNP-bound DppBCDF adopts an inward-facing conformation, similar to that of apo-DppBCDF, with only one ATPγS or AMPPNP molecule bound to DppF. By contrast, ATPγS-bound DppABCDF adopts an outward-facing conformation, with two ATPγS molecules glueing DppD and DppF at the interface. Consistent with structural observations, ATPase activity assays show that the DppBCDF translocator itself is inactive and its activation requires concurrent binding of DppA and ATP. In addition, bacterial complementation experiments imply that a unique periplasmic scoop motif in DppB may play important roles in ensuring dipeptide substrates import across the membrane, presumably by preventing dipeptide back-and-forth binding to DppA and avoiding dipeptides escaping into the periplasm upon being released from DppA.
History
DepositionApr 12, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39739.png

Downloads & links

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Map

FileDownload / File: emd_39739.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.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0016774915 - 2.9121268
Average (Standard dev.)0.0007689381 (±0.020265386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39739_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #1

Fileemd_39739_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : DppBCDF bound to AMPPNP

EntireName: DppBCDF bound to AMPPNP
Components
  • Complex: DppBCDF bound to AMPPNP
    • Protein or peptide: Dipeptide transport system permease protein DppB
    • Protein or peptide: Dipeptide transport system permease protein DppC
    • Protein or peptide: Dipeptide transport ATP-binding protein DppD
    • Protein or peptide: Dipeptide transport ATP-binding protein DppF
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: DppBCDF bound to AMPPNP

SupramoleculeName: DppBCDF bound to AMPPNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 143 KDa

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Macromolecule #1: Dipeptide transport system permease protein DppB

MacromoleculeName: Dipeptide transport system permease protein DppB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 37.531812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLQFILRRLG LVIPTFIGIT LLTFAFVHMI PGDPVMIMAG ERGISPERHA QLLAELGLDK PMWQQYLHYI WGVMHGDLGI SMKSRIPVW EEFVPRFQAT LELGVCAMIF ATAVGIPVGV LAAVKRGSIF DHTAVGLALT GYSMPIFWWG MMLIMLVSVH W NLTPVSGR ...String:
MLQFILRRLG LVIPTFIGIT LLTFAFVHMI PGDPVMIMAG ERGISPERHA QLLAELGLDK PMWQQYLHYI WGVMHGDLGI SMKSRIPVW EEFVPRFQAT LELGVCAMIF ATAVGIPVGV LAAVKRGSIF DHTAVGLALT GYSMPIFWWG MMLIMLVSVH W NLTPVSGR VSDMVFLDDS NPLTGFMLID TAIWGEDGNF IDAVAHMILP AIVLGTIPLA VIVRMTRSSM LEVLGEDYIR TA RAKGLTR MRVIIVHALR NAMLPVVTVI GLQVGTLLAG AILTETIFSW PGLGRWLIDA LQRRDYPVVQ GGVLLVATMI ILV NLLVDL LYGVVNPRIR HKK

UniProtKB: Dipeptide transport system permease protein DppB

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Macromolecule #2: Dipeptide transport system permease protein DppC

MacromoleculeName: Dipeptide transport system permease protein DppC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 32.328295 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQVTENKVI SAPVPMTPLQ EFWHYFKRNK GAVVGLVYVV IVLFIAIFAN WIAPYNPAEQ FRDALLAPPA WQEGGSMAHL LGTDDVGRD VLSRLMYGAR LSLLVGCLVV VLSLIMGVIL GLIAGYFGGL VDNIIMRVVD IMLALPSLLL ALVLVAIFGP S IGNAALAL ...String:
MSQVTENKVI SAPVPMTPLQ EFWHYFKRNK GAVVGLVYVV IVLFIAIFAN WIAPYNPAEQ FRDALLAPPA WQEGGSMAHL LGTDDVGRD VLSRLMYGAR LSLLVGCLVV VLSLIMGVIL GLIAGYFGGL VDNIIMRVVD IMLALPSLLL ALVLVAIFGP S IGNAALAL TFVALPHYVR LTRAAVLVEV NRDYVTASRV AGAGAMRQMF INIFPNCLAP LIVQASLGFS NAILDMAALG FL GMGAQPP TPEWGTMLSD VLQFAQSAWW VVTFPGLAIL LTVLAFNLMG DGLRDALDPK LKQ

UniProtKB: Dipeptide transport system permease protein DppC

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Macromolecule #3: Dipeptide transport ATP-binding protein DppD

MacromoleculeName: Dipeptide transport ATP-binding protein DppD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type dipeptide transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 35.886363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALLNVDKLS VHFGDESAPF RAVDRISYSV KQGEVVGIVG ESGSGKSVSS LAIMGLIDYP GRVMAEKLEF NGQDLQRISE KERRNLVGA EVAMIFQDPM TSLNPCYTVG FQIMEAIKVH QGGNKSTRRQ RAIDLLNQVG IPDPASRLDV YPHQLSGGMS Q RVMIAMAI ...String:
MALLNVDKLS VHFGDESAPF RAVDRISYSV KQGEVVGIVG ESGSGKSVSS LAIMGLIDYP GRVMAEKLEF NGQDLQRISE KERRNLVGA EVAMIFQDPM TSLNPCYTVG FQIMEAIKVH QGGNKSTRRQ RAIDLLNQVG IPDPASRLDV YPHQLSGGMS Q RVMIAMAI ACRPKLLIAD QPTTALDVTI QAQIIELLLE LQQKENMALV LITHDLALVA EAAHKIIVMY AGQVVETGDA HA IFHAPRH PYTQALLRAL PEFAQDKERL ASLPGVVPGK YDRPNGCLLN PRCPYATDRC RAEEPALNML ADGRQSKCHY PLD DAGRPT L

UniProtKB: Dipeptide transport ATP-binding protein DppD

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Macromolecule #4: Dipeptide transport ATP-binding protein DppF

MacromoleculeName: Dipeptide transport ATP-binding protein DppF / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type dipeptide transporter
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 37.610453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSTQEATLQQ PLLQAIDLKK HYPVKKGMFA PERLVKALDG VSFNLERGKT LAVVGESGCG KSTLGRLLTM IEMPTGGELY YQGQDLLKH DPQAQKLRRQ KIQIVFQNPY GSLNPRKKVG QILEEPLLIN TSLSKEQRRE KALSMMAKVG LKTEHYDRYP H MFSGGQRQ ...String:
MSTQEATLQQ PLLQAIDLKK HYPVKKGMFA PERLVKALDG VSFNLERGKT LAVVGESGCG KSTLGRLLTM IEMPTGGELY YQGQDLLKH DPQAQKLRRQ KIQIVFQNPY GSLNPRKKVG QILEEPLLIN TSLSKEQRRE KALSMMAKVG LKTEHYDRYP H MFSGGQRQ RIAIARGLML DPDVVIADQP VSALDVSVRA QVLNLMMDLQ QELGLSYVFI SHDLSVVEHI ADEVMVMYLG RC VEKGTKD QIFNNPRHPY TQALLSATPR LNPDDRRERI KLSGELPSPL NPPPGCAFNA RCRRRFGPCT QLQPQLKDYG GQL VACFAV DQDENPQR

UniProtKB: Dipeptide transport ATP-binding protein DppF

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 596321
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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