[English] 日本語
Yorodumi
- PDB-5trg: Structure of Mycobacterium tuberculosis proteasome in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5trg
TitleStructure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide DPLG-2
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/HYDROLASE inhibitor / N / C-capped dipeptides / Mycobacterium tuberculosis / DPLG-2 / 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~-[(2E)-3-phenylprop-2-enoyl]-L-asparaginyl-4-fluoro-N-[(naphthalen-1-yl)methyl]-L-phenylalaninamide / Chem-7HJ / 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: 2.804 Å
AuthorsHsu, H.-C. / Fan, H. / Singh, R.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 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Aug 12, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.5Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)726,16642
Polymers717,44728
Non-polymers8,71814
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.045, 219.087, 137.894
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
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-7HJ / N,N-diethyl-N~2~-[(2E)-3-phenylprop-2-enoyl]-L-asparaginyl-4-fluoro-N-[(naphthalen-1-yl)methyl]-L-phenylalaninamide


Type: Non-polymer / Class: Inhibitor / Mass: 622.728 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C37H39FN4O4
References: N,N-diethyl-N~2~-[(2E)-3-phenylprop-2-enoyl]-L-asparaginyl-4-fluoro-N-[(naphthalen-1-yl)methyl]-L-phenylalaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate (pH 6.2), 14% PEG-3350,

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 167090 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 48.6003639492 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.776 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HFA

3hfa


Resolution: 2.804→49.53 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 8301 4.97 %
Rwork0.1604 --
obs0.1632 167057 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.804→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46384 0 644 329 47357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01447743
X-RAY DIFFRACTIONf_angle_d1.29264583
X-RAY DIFFRACTIONf_dihedral_angle_d18.22428443
X-RAY DIFFRACTIONf_chiral_restr0.0737285
X-RAY DIFFRACTIONf_plane_restr0.0098490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8041-2.83590.32482430.24854665X-RAY DIFFRACTION88
2.8359-2.86930.33282740.24055204X-RAY DIFFRACTION98
2.8693-2.90430.34792830.22915220X-RAY DIFFRACTION99
2.9043-2.9410.30192780.21575294X-RAY DIFFRACTION99
2.941-2.97970.2962900.19915294X-RAY DIFFRACTION100
2.9797-3.02050.26262650.19585250X-RAY DIFFRACTION100
3.0205-3.06370.26482830.19455342X-RAY DIFFRACTION100
3.0637-3.10940.26333040.19655232X-RAY DIFFRACTION100
3.1094-3.1580.2552800.19615399X-RAY DIFFRACTION100
3.158-3.20980.26293090.18725232X-RAY DIFFRACTION100
3.2098-3.26510.24832560.18215294X-RAY DIFFRACTION100
3.2651-3.32450.25272820.18485356X-RAY DIFFRACTION100
3.3245-3.38840.24992900.18325273X-RAY DIFFRACTION100
3.3884-3.45750.24092620.17945361X-RAY DIFFRACTION100
3.4575-3.53270.22712810.17135321X-RAY DIFFRACTION100
3.5327-3.61490.22922550.16495297X-RAY DIFFRACTION100
3.6149-3.70520.23752760.16975310X-RAY DIFFRACTION100
3.7052-3.80540.22232830.16015330X-RAY DIFFRACTION100
3.8054-3.91730.20342800.15615313X-RAY DIFFRACTION100
3.9173-4.04370.20932840.15385331X-RAY DIFFRACTION100
4.0437-4.18810.20222630.15665305X-RAY DIFFRACTION100
4.1881-4.35570.2082840.14415324X-RAY DIFFRACTION100
4.3557-4.55380.18212860.13685307X-RAY DIFFRACTION100
4.5538-4.79370.16152820.12945364X-RAY DIFFRACTION100
4.7937-5.09380.17362670.12815330X-RAY DIFFRACTION100
5.0938-5.48660.19482900.13895330X-RAY DIFFRACTION100
5.4866-6.03790.19162690.15195351X-RAY DIFFRACTION100
6.0379-6.90960.21792740.14775347X-RAY DIFFRACTION100
6.9096-8.69770.13242780.11175365X-RAY DIFFRACTION100
8.6977-49.53790.16232500.14675415X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more