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- PDB-8j5u: Crystal structure of Mycobacterium tuberculosis OppA complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8j5u
TitleCrystal structure of Mycobacterium tuberculosis OppA complexed with an endogenous oligopeptide
Components
  • Endogenous oligopeptide
  • Uncharacterized protein Rv1280c
KeywordsPEPTIDE BINDING PROTEIN / OppA / Oligopeptide binding protein / Cluster C SBP / Mycobacterium tuberculosis
Function / homology
Function and homology information


Tolerance by Mtb to nitric oxide produced by macrophages / glutathione binding / peptide transport / peptide transmembrane transporter activity / protein import / ATP-binding cassette (ABC) transporter complex / peptide binding / outer membrane-bounded periplasmic space / periplasmic space / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
Uncharacterized protein Rv1280c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Rv1280c
B: Endogenous oligopeptide


Theoretical massNumber of molelcules
Total (without water)65,5232
Polymers65,5232
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.643, 56.986, 101.902
Angle α, β, γ (deg.)90.00, 122.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein Rv1280c / Oligopeptide-binding protein OppA


Mass: 64609.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Author stated: The data collection statistics was calculated within the same resolution range as the refinement. The number of collected unique reflections was 39151. After anisotropic ...Details: Author stated: The data collection statistics was calculated within the same resolution range as the refinement. The number of collected unique reflections was 39151. After anisotropic correction using the STARANISO server and refinement using PHENIX, the number of unique reflections was 29132.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv1280c, MTCY50.02
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WGU5
#2: Protein/peptide Endogenous oligopeptide


Mass: 913.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES (pH 7.5), 24% (w/v) polyethylene glycol 1500 (PEG1500), 200 mM L-proline.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 39151 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.146 / Net I/σ(I): 10.51
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.98-2.031.06928530.8071.1631
2.03-2.090.88727720.870.961
2.09-2.150.74227410.9030.8021
2.15-2.220.60426580.9290.6541
2.22-2.290.49125800.9470.5331
2.29-2.370.43624740.9550.4731
2.37-2.460.35924260.9730.3881
2.46-2.560.29122910.980.3161
2.56-2.670.24822280.9850.2681
2.67-2.80.21121440.990.2271
2.8-2.950.15820140.9930.1711
2.95-3.130.12519210.9950.1361
3.13-3.350.10318010.9960.1121
3.35-3.620.07916820.9970.0861
3.62-3.960.06415420.9980.0691
3.96-4.430.05314120.9980.0571
4.43-5.120.05212410.9980.0561
5.12-6.270.05210690.9980.0571
6.27-8.860.0448270.9990.0471
8.86-500.0354750.9990.0381

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→48.88 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.226 2014 -
Rwork0.181 --
obs-29132 99.5 %
Refinement stepCycle: LAST / Resolution: 1.98→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 0 241 4380
LS refinement shellResolution: 1.98→2.03 Å
RfactorNum. reflection% reflection
Rfree0.2185 --
Rwork0.1877 --
obs-947 34 %

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