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- EMDB-39741: Cryo-EM structure of Escherichia coli DppAR383D+D436RBCDF in pre-... -

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Basic information

Entry
Database: EMDB / ID: EMD-39741
TitleCryo-EM structure of Escherichia coli DppAR383D+D436RBCDF in pre-catalytic state
Map data
Sample
  • Complex: DppAR383DD436RBCDF bound to ATPgammaS
    • 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
    • Protein or peptide: Dipeptide-binding protein
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsABC importer / SBP / Peptide transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type dipeptide transporter / dipeptide transport / heme transport / dipeptide transmembrane transporter activity / heme transmembrane transporter activity / heme transmembrane transport / peptide transmembrane transporter activity / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : ...ABC-type dipeptide transporter / dipeptide transport / heme transport / dipeptide transmembrane transporter activity / heme transmembrane transporter activity / heme transmembrane transport / peptide transmembrane transporter activity / positive chemotaxis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / peptide binding / response to radiation / protein transport / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / heme 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 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 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / 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-binding protein / 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: 3.26 Å
AuthorsLi P / Huang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Cryo-EM structure of Escherichia coli DppAR383DD436RBCDF in the catalytic intermediate state
Authors: Li P / Huang Y
History
DepositionApr 12, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39741.png

Downloads & links

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Map

FileDownload / File: emd_39741.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 399.36 Å		1.04 Å/pix.
x 384 pix.
= 399.36 Å		1.04 Å/pix.
x 384 pix.
= 399.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0016944591 - 2.3873303
Average (Standard dev.)0.00046194432 (±0.015904266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 399.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39741_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39741_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 : DppAR383DD436RBCDF bound to ATPgammaS

EntireName: DppAR383DD436RBCDF bound to ATPgammaS
Components
  • Complex: DppAR383DD436RBCDF bound to ATPgammaS
    • 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
    • Protein or peptide: Dipeptide-binding protein
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: DppAR383DD436RBCDF bound to ATPgammaS

SupramoleculeName: DppAR383DD436RBCDF bound to ATPgammaS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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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 (strain K12) (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: Dipeptide-binding protein

MacromoleculeName: Dipeptide-binding protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 60.366531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRISLKKSGM LKLGLSLVAM TVAASVQAKT LVYCSEGSPE GFNPQLFTSG TTYDASSVPL YNRLVEFKIG TTEVIPGLAE KWEVSEDGK TYTFHLRKGV KWHDNKEFKP TRELNADDVV FSFDRQKNAQ NPYHKVSGGS YEYFEGMGLP ELISEVKKVD D NTVQFVLT ...String:
MRISLKKSGM LKLGLSLVAM TVAASVQAKT LVYCSEGSPE GFNPQLFTSG TTYDASSVPL YNRLVEFKIG TTEVIPGLAE KWEVSEDGK TYTFHLRKGV KWHDNKEFKP TRELNADDVV FSFDRQKNAQ NPYHKVSGGS YEYFEGMGLP ELISEVKKVD D NTVQFVLT RPEAPFLADL AMDFASILSK EYADAMMKAG TPEKLDLNPI GTGPFQLQQY QKDSRIRYKA FDGYWGTKPQ ID TLVFSIT PDASVRYAKL QKNECQVMPY PNPADIARMK QDKSINLMEM PGLNVGYLSY NVQKKPLDDV KVRQALTYAV NKD AIIKAV YQGAGVSAKN LIPPTMWGYN DDVQDYTYDP EKAKALLKEA GLEKGFSIDL WAMPVQDPYN PNARRMAEMI QADW AKVGV QAKIVTYEWG EYLKRAKDGE HQTVMMGWTG RNGDPDNFFA TLFSCAASEQ GSNYSKWCYK PFEDLIQPAR ATDDH NKRV ELYKQAQVVM HDQAPALIIA HSTVFEPVRK EVKGYVVDPL GKHHFENVSI E

UniProtKB: Dipeptide-binding protein

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #7: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 375658
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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