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- PDB-8j5s: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pr... -

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Basic information

Entry
Database: PDB / ID: 8j5s
TitleCryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state
Components
  • (Putative peptide transport permease protein ...) x 2
  • (Uncharacterized ...) x 2
  • Endogenous oligopeptide
KeywordsMEMBRANE PROTEIN / OppABCD / AMPPNP-Mg / Pre-catalytic intermediate state / Type I ABC importer
Function / homology
Function and homology information


peptidoglycan peptide transmembrane transporter activity / ABC-type oligopeptide transporter / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / protein import / peptide transport / peptide transmembrane transporter activity / transmembrane transporter activity / peptide binding / ATP-binding cassette (ABC) transporter complex ...peptidoglycan peptide transmembrane transporter activity / ABC-type oligopeptide transporter / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / protein import / peptide transport / peptide transmembrane transporter activity / transmembrane transporter activity / peptide binding / ATP-binding cassette (ABC) transporter complex / peptidoglycan-based cell wall / transmembrane transport / protein transport / periplasmic space / ATP hydrolysis activity / ATP binding / 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 / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily ...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. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / Oligopeptide transport system permease protein OppB / Oligopeptide transport system permease protein OppC / Oligopeptide-binding protein OppA / Oligopeptide transport ATP-binding protein OppD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsYang, X. / Hu, T. / Zhang, B. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200996 China
National Natural Science Foundation of China (NSFC)32171217 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.
Authors: Xiaolin Yang / Tianyu Hu / Jingxi Liang / Zhiqi Xiong / Zhenli Lin / Yao Zhao / Xiaoting Zhou / Yan Gao / Shan Sun / Xiuna Yang / Luke W Guddat / Haitao Yang / Zihe Rao / Bing Zhang /
Abstract: Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD ...Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.
History
DepositionApr 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
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Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Rv1280c
B: Putative peptide transport permease protein Rv1283c
C: Putative peptide transport permease protein Rv1282c
D: Uncharacterized ABC transporter ATP-binding protein Rv1281c
E: Endogenous oligopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,47810
Polymers197,0655
Non-polymers1,4135
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Uncharacterized ... , 2 types, 2 molecules AD

#1: Protein Uncharacterized protein Rv1280c


Mass: 64501.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1280c, MTCY50.02
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WGU5
#4: Protein Uncharacterized ABC transporter ATP-binding protein Rv1281c


Mass: 65342.793 Da / Num. of mol.: 1 / Mutation: E180D,E525D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1281c, MTCY50.01
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WQJ5

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Putative peptide transport permease protein ... , 2 types, 2 molecules BC

#2: Protein Putative peptide transport permease protein Rv1283c


Mass: 35120.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1283c, MTCY373.02c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WFZ7
#3: Protein Putative peptide transport permease protein Rv1282c


Mass: 31402.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1282c, MTCY373.01c, MTCY3H3.01
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WFZ9

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Protein/peptide , 1 types, 1 molecules E

#5: Protein/peptide Endogenous oligopeptide


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)

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Non-polymers , 3 types, 5 molecules

#6: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / 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: Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state
Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169227 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00713527
ELECTRON MICROSCOPYf_angle_d0.7518441
ELECTRON MICROSCOPYf_dihedral_angle_d27.5491935
ELECTRON MICROSCOPYf_chiral_restr0.0472179
ELECTRON MICROSCOPYf_plane_restr0.0052379

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