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- PDB-8wdb: Cryo-EM structure of the ATP-bound DppABCD complex -

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Basic information

Entry
Database: PDB / ID: 8wdb
TitleCryo-EM structure of the ATP-bound DppABCD complex
Components
  • (Probable dipeptide-transport integral membrane protein ABC transporter ...) x 2
  • Probable dipeptide-transport ATP-binding protein ABC transporter DppD
  • Probable periplasmic dipeptide-binding lipoprotein DppA
KeywordsMEMBRANE PROTEIN / DppABCD / ABC importer / Mycobacterium tuberculosis
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 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
ADENOSINE-5'-TRIPHOSPHATE / 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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHu, T. / Zhang, B. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the ATP-bound DppABCD complex
Authors: Hu, T. / Zhang, B. / Rao, Z.
History
DepositionSep 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Probable dipeptide-transport ATP-binding protein ABC transporter DppD
B: Probable dipeptide-transport integral membrane protein ABC transporter DppB
C: Probable dipeptide-transport integral membrane protein ABC transporter DppC
A: Probable periplasmic dipeptide-binding lipoprotein DppA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1888
Polymers178,1254
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules DA

#1: Protein Probable dipeptide-transport ATP-binding protein ABC transporter DppD


Mass: 59018.547 Da / Num. of mol.: 1 / Mutation: E179Q,E457Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: dppD, Rv3663c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I6Y482
#4: Protein Probable periplasmic dipeptide-binding lipoprotein DppA


Mass: 56057.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: dppA, Rv3666c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I6X811

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Probable dipeptide-transport integral membrane protein ABC transporter ... , 2 types, 2 molecules BC

#2: Protein Probable dipeptide-transport integral membrane protein ABC transporter DppB


Mass: 32563.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: dppB, Rv3665c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I6YGV9
#3: Protein Probable dipeptide-transport integral membrane protein ABC transporter DppC


Mass: 30485.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: dppC, Rv3664c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: L0TEV4

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DppABCD / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65444 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00712588
ELECTRON MICROSCOPYf_angle_d0.74917197
ELECTRON MICROSCOPYf_dihedral_angle_d13.1237451
ELECTRON MICROSCOPYf_chiral_restr0.0482004
ELECTRON MICROSCOPYf_plane_restr0.0052229

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