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- PDB-8z1z: Cryo-EM structure of Escherichia coli DppAR383D+D436RBCDF in pre-... -

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Basic information

Entry
Database: PDB / ID: 8z1z
TitleCryo-EM structure of Escherichia coli DppAR383D+D436RBCDF in pre-catalytic state
Components
  • (Dipeptide transport ATP-binding protein ...) x 2
  • (Dipeptide transport system permease protein ...) x 2
  • Dipeptide-binding protein
KeywordsTRANSPORT PROTEIN / ABC importer / SBP / Peptide transporter
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / 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 K-12 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsLi, P. / Huang, Y.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptide transport system permease protein DppB
B: Dipeptide transport system permease protein DppC
C: Dipeptide transport ATP-binding protein DppD
D: Dipeptide transport ATP-binding protein DppF
F: Dipeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,4739
Polymers203,7235
Non-polymers1,7504
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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Dipeptide transport system permease protein ... , 2 types, 2 molecules AB

#1: Protein Dipeptide transport system permease protein DppB


Mass: 37531.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppB, b3543, JW3512 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEF8
#2: Protein Dipeptide transport system permease protein DppC


Mass: 32328.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppC, b3542, JW3511 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEG1

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Dipeptide transport ATP-binding protein ... , 2 types, 2 molecules CD

#3: Protein Dipeptide transport ATP-binding protein DppD


Mass: 35886.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppD, b3541, JW3510 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAG0, ABC-type dipeptide transporter
#4: Protein Dipeptide transport ATP-binding protein DppF


Mass: 37610.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: dppF, dppE, b3540, JW3509 / Production host: Escherichia coli (E. coli) / References: UniProt: P37313, ABC-type dipeptide transporter

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Protein , 1 types, 1 molecules F

#5: Protein Dipeptide-binding protein / DBP / Periplasmic dipeptide transport protein


Mass: 60366.531 Da / Num. of mol.: 1 / Mutation: R383D, D436R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dppA, b3544, JW3513 / Production host: Escherichia coli (E. coli) / References: UniProt: P23847

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: DppAR383DD436RBCDF bound to ATPgammaS / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375658 / Symmetry type: POINT

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