[English] 日本語
Yorodumi
- PDB-6bba: Crystal structure of human mitochondrial ClpP complex with acylde... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bba
TitleCrystal structure of human mitochondrial ClpP complex with acyldepsipeptide ADEP-28
Components
  • ATP-dependent Clp protease proteolytic subunit, mitochondrial
  • Acyldepsipeptide ADEP-28
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protease / proteostasis / protein quality control / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Cell Chem Biol / Year: 2018
Title: Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death.
Authors: Wong, K.S. / Mabanglo, M.F. / Seraphim, T.V. / Mollica, A. / Mao, Y.Q. / Rizzolo, K. / Leung, E. / Moutaoufik, M.T. / Hoell, L. / Phanse, S. / Goodreid, J. / Barbosa, L.R.S. / Ramos, C.H.I. ...Authors: Wong, K.S. / Mabanglo, M.F. / Seraphim, T.V. / Mollica, A. / Mao, Y.Q. / Rizzolo, K. / Leung, E. / Moutaoufik, M.T. / Hoell, L. / Phanse, S. / Goodreid, J. / Barbosa, L.R.S. / Ramos, C.H.I. / Babu, M. / Mennella, V. / Batey, R.A. / Schimmer, A.D. / Houry, W.A.
History
DepositionOct 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 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 / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
H: Acyldepsipeptide ADEP-28
I: Acyldepsipeptide ADEP-28
J: Acyldepsipeptide ADEP-28
K: Acyldepsipeptide ADEP-28
L: Acyldepsipeptide ADEP-28
M: Acyldepsipeptide ADEP-28
N: Acyldepsipeptide ADEP-28


Theoretical massNumber of molelcules
Total (without water)174,89414
Polymers174,89414
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, assembly also confirmed by SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31870 Å2
ΔGint-95 kcal/mol
Surface area51320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.399, 172.399, 135.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit, mitochondrial / Endopeptidase Clp


Mass: 24179.875 Da / Num. of mol.: 7 / Fragment: residues 58-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q16740, endopeptidase Clp
#2: Protein/peptide
Acyldepsipeptide ADEP-28


Mass: 804.920 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate pH 4.6, 4% w/v polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.796→50 Å / Num. obs: 57827 / % possible obs: 99.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.056 / Rrim(I) all: 0.188 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2896 / Rpim(I) all: 0.566 / Rrim(I) all: 0.188 / Χ2: 0.684 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TG6

1tg6


Resolution: 2.796→46.735 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2017 3.49 %
Rwork0.1866 --
obs0.1883 57827 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.796→46.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10233 0 392 208 10833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910856
X-RAY DIFFRACTIONf_angle_d1.18114718
X-RAY DIFFRACTIONf_dihedral_angle_d24.9044094
X-RAY DIFFRACTIONf_chiral_restr0.0621686
X-RAY DIFFRACTIONf_plane_restr0.0071860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7956-2.86550.34711430.30733892X-RAY DIFFRACTION99
2.8655-2.9430.32451410.2713956X-RAY DIFFRACTION100
2.943-3.02950.32041410.23673961X-RAY DIFFRACTION100
3.0295-3.12730.28131430.2343967X-RAY DIFFRACTION100
3.1273-3.23910.33291450.22813958X-RAY DIFFRACTION100
3.2391-3.36870.31421420.23083953X-RAY DIFFRACTION100
3.3687-3.5220.27971450.21063961X-RAY DIFFRACTION100
3.522-3.70760.2591420.18043982X-RAY DIFFRACTION100
3.7076-3.93980.20721430.17193985X-RAY DIFFRACTION100
3.9398-4.24380.18751440.15563998X-RAY DIFFRACTION100
4.2438-4.67050.19751480.14574014X-RAY DIFFRACTION100
4.6705-5.34550.20541450.15994001X-RAY DIFFRACTION100
5.3455-6.73160.23791450.19164054X-RAY DIFFRACTION100
6.7316-46.74140.19451500.1754128X-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