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- EMDB-37459: Cryo-EM structure of the substrate-bound DppABCD complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37459
TitleCryo-EM structure of the substrate-bound DppABCD complex
Map data
Sample
  • Complex: DppABCD
    • Protein or peptide: Probable periplasmic dipeptide-binding lipoprotein DppA
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppB
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppC
    • Protein or peptide: tetrapeptide
    • Protein or peptide: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
KeywordsDppABCD / ABC importer / Mycobacterium tuberculosis / MEMBRANE PROTEIN
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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 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. / 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
Probable periplasmic dipeptide-binding lipoprotein DppA / Probable dipeptide-transport ATP-binding protein ABC transporter DppD / Probable dipeptide-transport integral membrane protein ABC transporter DppB / Probable dipeptide-transport integral membrane protein ABC transporter DppC
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / Mycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsHu T / Zhang B / Rao Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the substrate-bound DppABCD complex
Authors: Hu T / Zhang B / Rao Z
History
DepositionSep 14, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37459.png

Downloads & links

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Map

FileDownload / File: emd_37459.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.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-1.2906142 - 2.1707957
Average (Standard dev.)-0.0012472518 (±0.05642572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37459_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_37459_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 : DppABCD

EntireName: DppABCD
Components
  • Complex: DppABCD
    • Protein or peptide: Probable periplasmic dipeptide-binding lipoprotein DppA
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppB
    • Protein or peptide: Probable dipeptide-transport integral membrane protein ABC transporter DppC
    • Protein or peptide: tetrapeptide
    • Protein or peptide: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

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Supramolecule #1: DppABCD

SupramoleculeName: DppABCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Macromolecule #1: Probable periplasmic dipeptide-binding lipoprotein DppA

MacromoleculeName: Probable periplasmic dipeptide-binding lipoprotein DppA
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 56.057242 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: CGGGVLSPDV VLVNGGEPPN PLIPTGTNDS NGGRIIDRLF AGLMSYDAVG KPSLEVAQSI ESADNVNYRI TVKPGWKFTD GSPVTAHSF VDAWNYGALS TNAQLQQHFF SPIEGFDDVA GAPGDKSRTT MSGLRVVNDL EFTVRLKAPT IDFTLRLGHS S FYPLPDSA ...String:
CGGGVLSPDV VLVNGGEPPN PLIPTGTNDS NGGRIIDRLF AGLMSYDAVG KPSLEVAQSI ESADNVNYRI TVKPGWKFTD GSPVTAHSF VDAWNYGALS TNAQLQQHFF SPIEGFDDVA GAPGDKSRTT MSGLRVVNDL EFTVRLKAPT IDFTLRLGHS S FYPLPDSA FRDMAAFGRN PIGNGPYKLA DGPAGPAWEH NVRIDLVPNP DYHGNRKPRN KGLRFEFYAN LDTAYADLLS GN LDVLDTI PPSALTVYQR DLGDHATSGP AAINQTLDTP LRLPHFGGEE GRLRRLALSA AINRPQICQQ IFAGTRSPAR DFT ARSLPG FDPNLPGNEV LDYDPQRARR LWAQADAISP WSGRYAIAYN ADAGHRDWVD AVANSIKNVL GIDAVAAPQP TFAG FRTQI TNRAIDSAFR AGWRGDYPSM IEFLAPLFTA GAGSNDVGYI NPEFDAALAA AEAAPTLTES HELVNDAQRI LFHDM PVVP LWDYISVVGW SSQVSNVTVT WNGLPDYENI VKA

UniProtKB: Probable periplasmic dipeptide-binding lipoprotein DppA

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Macromolecule #2: Probable dipeptide-transport integral membrane protein ABC transp...

MacromoleculeName: Probable dipeptide-transport integral membrane protein ABC transporter DppB
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 32.563557 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MGWYVARRVA VMVPVFLGAT LLIYGMVFLL PGDPVAALAG DRPLTPAVAA QLRSHYHLDD PFLVQYLRYL GGILHGDLGR AYSGLPVSA VLAHAFPVTI RLALIALAVE AVLGIGFGVI AGLRQGGIFD SAVLVTGLVI IAIPIFVLGF LAQFLFGVQL E IAPVTVGE ...String:
MGWYVARRVA VMVPVFLGAT LLIYGMVFLL PGDPVAALAG DRPLTPAVAA QLRSHYHLDD PFLVQYLRYL GGILHGDLGR AYSGLPVSA VLAHAFPVTI RLALIALAVE AVLGIGFGVI AGLRQGGIFD SAVLVTGLVI IAIPIFVLGF LAQFLFGVQL E IAPVTVGE RASVGRLLLP GIVLGAMSFA YVVRLTRSAV AANAHADYVR TATAKGLSRP RVVTVHILRN SLIPVVTFLG AD LGALMGG AIVTEGIFNI HGVGGVLYQA VTRQETPTVV SIVTVLVLIY LITNLLVDLL YAALDPRIRY G

UniProtKB: Probable dipeptide-transport integral membrane protein ABC transporter DppB

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Macromolecule #3: Probable dipeptide-transport integral membrane protein ABC transp...

MacromoleculeName: Probable dipeptide-transport integral membrane protein ABC transporter DppC
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 30.48573 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MAEHTGFWLD AWRGLRRRPK FVIAAALILL ILVVAAFPSL FTAADPTYAD PSQSMLAPSA AHWFGTDLQG HDIYSRTVYG ARASVTVGL GATLAVFVVG GALGALAGFY GSWIDAVVSR VTDVFLGLPL LLAAIVLMQV MHHRTVWTVI AILALFGWPQ V ARIARGAV ...String:
MAEHTGFWLD AWRGLRRRPK FVIAAALILL ILVVAAFPSL FTAADPTYAD PSQSMLAPSA AHWFGTDLQG HDIYSRTVYG ARASVTVGL GATLAVFVVG GALGALAGFY GSWIDAVVSR VTDVFLGLPL LLAAIVLMQV MHHRTVWTVI AILALFGWPQ V ARIARGAV LEVRASDYVL AAKALGLNRF QILLRHALPN AVGPVIAVAT VALGIFIVTE ATLSYLGVGL PTSVVSWGGD IN VAQTRLR SGSPILFYPA GALAITVLAF MMMGDALRDA LDPASRAWRA

UniProtKB: Probable dipeptide-transport integral membrane protein ABC transporter DppC

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Macromolecule #4: tetrapeptide

MacromoleculeName: tetrapeptide / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 330.379 Da
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
AVAA

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Macromolecule #5: Probable dipeptide-transport ATP-binding protein ABC transporter DppD

MacromoleculeName: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Molecular weightTheoretical: 59.020516 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSVPAAPLLS VEGLEVTFGT DAPAVCGVDL AVRSGQTVAV VGESGSGKST TAAAILGLLP AGGRITAGRV VFDGRDITGA DAKRLRSIR GREIGYVPQD PMTNLNPVWK VGFQVTEALR ANTDGRAARR RAVELLAEAG LPDPAKQAGR YPHQLSGGMC Q RALIAIGL ...String:
MSVPAAPLLS VEGLEVTFGT DAPAVCGVDL AVRSGQTVAV VGESGSGKST TAAAILGLLP AGGRITAGRV VFDGRDITGA DAKRLRSIR GREIGYVPQD PMTNLNPVWK VGFQVTEALR ANTDGRAARR RAVELLAEAG LPDPAKQAGR YPHQLSGGMC Q RALIAIGL AGRPRLLIAD EPTSALDVTV QRQVLDHLQG LTDELGTALL LITHDLALAA QRAEAVVVVR RGVVVESGAA QS ILQSPQH EYTRRLVAAA PSLTARSRRP PESRSRATTQ AGDILVVSEL TKIYRESRGA PWRRVESRAV DGVSFRLPRA STL AIVGES GSGKSTLARM VLGLLQPTSG TVVFDGTYDV GALARDQVLA FRRRVQPVFQ NPYSSLDPMY SVFRAIEEPL RVHH VGDRR QRQRAVRELV DQVALPSSIL GRRPRELSGG QRQRVAIARA LALRPEVLVC DEAVSALDVL VQAQILDLLA DLQAD LGLT YLFISHDLAV IRQIADDVLV MRAGRVVEHA STEEVFSRPR HEYTRQLLQA IPGAPSAPRK VGNL

UniProtKB: Probable dipeptide-transport ATP-binding protein ABC transporter DppD

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #7: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 7 / Number of copies: 1 / Formula: 9XX
Molecular weightTheoretical: 594.992 Da
Chemical component information

ChemComp-9XX:
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

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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 K3 (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: 2.2 µm / Nominal defocus min: 1.4000000000000001 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: 78401
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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