[English] 日本語
Yorodumi
- PDB-5ji2: HslU L199Q in HslUV complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ji2
TitleHslU L199Q in HslUV complex
Components
  • ATP-dependent protease ATPase subunit HslU
  • ATP-dependent protease subunit HslV
KeywordsHYDROLASE / AAA+ ATPase / peptidase
Function / homology
Function and homology information


HslU-HslV peptidase / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Aminohydrolase, N-terminal nucleophile (Ntn) domain ...Heat shock protein HslU / ATP-dependent protease, HslV subunit / : / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Helicase, Ruva Protein; domain 3 / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 4-Layer Sandwich / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent protease subunit HslV / ATP-dependent protease ATPase subunit HslU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.307 Å
AuthorsGrant, R.A. / Sauer, R.T. / Schmitz, K.R. / Baytshtok, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI016892-36 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM1011988-37 United States
Citation
Journal: Structure / Year: 2016
Title: A Structurally Dynamic Region of the HslU Intermediate Domain Controls Protein Degradation and ATP Hydrolysis.
Authors: Baytshtok, V. / Fei, X. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
#1: Journal: Structure / Year: 2001
Title: Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism.
Authors: Wang, J. / Song, J.J. / Franklin, M.C. / Kamtekar, S. / Im, Y.J. / Rho, S.H. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Eom, S.H.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence / Database references
Category: citation / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,82611
Polymers181,8996
Non-polymers9275
Water00
1
A: ATP-dependent protease subunit HslV
B: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4954
Polymers40,4462
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP-dependent protease subunit HslV
D: ATP-dependent protease subunit HslV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4703
Polymers40,4462
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ATP-dependent protease ATPase subunit HslU
F: ATP-dependent protease ATPase subunit HslU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8624
Polymers101,0072
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.005, 170.005, 163.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

-
Components

#1: Protein
ATP-dependent protease subunit HslV / Heat shock protein HslV


Mass: 20223.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria)
Strain: 55989 / EAEC / Gene: hslV, EC55989_4410 / Production host: Escherichia coli (E. coli) / References: UniProt: B7LA29, HslU-HslV peptidase
#2: Protein ATP-dependent protease ATPase subunit HslU / Heat shock protein HslU / Unfoldase HslU


Mass: 50503.551 Da / Num. of mol.: 2 / Mutation: L199Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: hslU, htpI, Z5478, ECs4858 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6H6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.17 % / Description: hexagonal plates
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 1.8 M Ammonium Sulfate, 7.5 mg/ml HslU(L199Q), 9.7 mg/ml HslV, 5 mM ATP, 0.5 mg/ml Arc-st11-ssrA (synthetic peptide substrate)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3.3→50 Å / Num. obs: 41171 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Χ2: 1.149 / Net I/av σ(I): 20.976 / Net I/σ(I): 6.2 / Num. measured all: 450056
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.3-3.369.81.5091100
3.36-3.4210.61.281100
3.42-3.48111.0891100
3.48-3.5511.10.8481100
3.55-3.6311.10.6971100
3.63-3.7211.10.4931100
3.72-3.8111.20.5191100
3.81-3.9111.20.3721100
3.91-4.0311.30.3281100
4.03-4.1611.20.2481100
4.16-4.3111.20.1971100
4.31-4.4811.20.1531100
4.48-4.6811.20.1251100
4.68-4.9311.20.1151100
4.93-5.2411.10.1161100
5.24-5.64110.1171100
5.64-6.21110.1181100
6.21-7.110.80.0951100
7.1-8.9410.50.0521100
8.94-50100.0381100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4A

1g4a


Resolution: 3.307→49.076 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.2811 2003 4.87 %
Rwork0.2356 --
obs0.2385 41171 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 202.4 Å2 / Biso mean: 125.4572 Å2 / Biso min: 48.3 Å2
Refinement stepCycle: final / Resolution: 3.307→49.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10975 0 81 0 11056
Biso mean--94.48 --
Num. residues----1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311165
X-RAY DIFFRACTIONf_angle_d0.54215086
X-RAY DIFFRACTIONf_chiral_restr0.0541777
X-RAY DIFFRACTIONf_plane_restr0.0031950
X-RAY DIFFRACTIONf_dihedral_angle_d19.514172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.309-3.39170.3671420.316827592901
3.3917-3.48340.32461390.315427492888
3.4834-3.58590.29381430.315927622905
3.5859-3.70150.33911440.320827812925
3.7015-3.83370.33891350.286627532888
3.8337-3.98710.32951430.266327782921
3.9871-4.16840.27061440.254927632907
4.1684-4.3880.28761430.240127782921
4.388-4.66260.28011430.211727762919
4.6626-5.02210.28251440.209328002944
5.0221-5.52650.27761420.219827912933
5.5265-6.3240.30321420.241628252967
6.324-7.9590.2281470.208828422989
7.959-42.50470.24491520.229653117

+
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