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- PDB-5trr: Structure of Mycobacterium tuberculosis proteasome in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5trr
TitleStructure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2169
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/HYDROLASE inhibitor / N / C-capped dipeptides / Mycobacterium tuberculosis / proteasome inhibitors / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-N-[(naphthalen-1-yl)methyl]-L-alaninamide / Chem-7HY / Proteasome subunit alpha / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.103 Å
AuthorsHsu, H.-C. / Fan, H. / Singh, P.K. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070285 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome.
Authors: Hsu, H.C. / Singh, P.K. / Fan, H. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector / _software.version
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Aug 12, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit alpha
Q: Proteasome subunit alpha
R: Proteasome subunit alpha
S: Proteasome subunit alpha
T: Proteasome subunit alpha
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)724,87742
Polymers717,44728
Non-polymers7,42914
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area84940 Å2
ΔGint-78 kcal/mol
Surface area217950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.297, 197.700, 165.184
Angle α, β, γ (deg.)90.00, 103.01, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PrcA


Mass: 25971.975 Da / Num. of mol.: 14 / Fragment: UNP residues 10-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, MRA_2124 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D5, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 25274.264 Da / Num. of mol.: 14 / Fragment: UNP residues 58-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcB, MRA_2125 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4D6, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex
#3: Chemical
ChemComp-7HY / N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-N-[(naphthalen-1-yl)methyl]-L-alaninamide


Type: Non-polymer / Class: Inhibitor / Mass: 530.658 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C31H38N4O4
References: N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-N-[(naphthalen-1-yl)methyl]-L-alaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate (pH 6.2) and 14% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.2473073393 Å / Num. obs: 131508 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 73.5256458866 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.775 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HFA

3hfa


Resolution: 3.103→47.247 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 6512 4.95 %
Rwork0.1705 --
obs0.1725 131472 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.103→47.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46311 0 546 62 46919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747557
X-RAY DIFFRACTIONf_angle_d0.77264329
X-RAY DIFFRACTIONf_dihedral_angle_d16.75428379
X-RAY DIFFRACTIONf_chiral_restr0.0527276
X-RAY DIFFRACTIONf_plane_restr0.0058460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.103-3.13820.29651070.26772424X-RAY DIFFRACTION56
3.1382-3.17510.33391740.25083623X-RAY DIFFRACTION83
3.1751-3.21390.33331660.24743740X-RAY DIFFRACTION88
3.2139-3.25450.30221990.23113929X-RAY DIFFRACTION91
3.2545-3.29730.28931900.23464025X-RAY DIFFRACTION94
3.2973-3.34250.26782320.23074187X-RAY DIFFRACTION98
3.3425-3.39020.29352570.2214175X-RAY DIFFRACTION99
3.3902-3.44080.25922320.21554297X-RAY DIFFRACTION99
3.4408-3.49460.242020.20654235X-RAY DIFFRACTION100
3.4946-3.55190.23982150.20414299X-RAY DIFFRACTION100
3.5519-3.61310.24422440.20854280X-RAY DIFFRACTION100
3.6131-3.67880.25062360.2154248X-RAY DIFFRACTION100
3.6788-3.74950.24322150.20134315X-RAY DIFFRACTION100
3.7495-3.8260.23262100.19054280X-RAY DIFFRACTION100
3.826-3.90910.24471820.17914315X-RAY DIFFRACTION100
3.9091-40.22512050.17144375X-RAY DIFFRACTION100
4-4.10.22472410.17124242X-RAY DIFFRACTION100
4.1-4.21080.19852520.16564273X-RAY DIFFRACTION100
4.2108-4.33460.20832570.16264288X-RAY DIFFRACTION100
4.3346-4.47440.20392490.1554259X-RAY DIFFRACTION100
4.4744-4.63420.19472410.15524288X-RAY DIFFRACTION100
4.6342-4.81960.19052260.14384279X-RAY DIFFRACTION100
4.8196-5.03870.17212330.14274298X-RAY DIFFRACTION100
5.0387-5.3040.17662150.14394301X-RAY DIFFRACTION100
5.304-5.63580.1992430.15584296X-RAY DIFFRACTION100
5.6358-6.07020.22422350.16884309X-RAY DIFFRACTION100
6.0702-6.67950.20422150.1694322X-RAY DIFFRACTION100
6.6795-7.64250.15692040.13044340X-RAY DIFFRACTION100
7.6425-9.61540.12742170.10994344X-RAY DIFFRACTION100
9.6154-47.25280.18022180.16324374X-RAY DIFFRACTION99

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