[English] 日本語
Yorodumi
- PDB-8ypa: Human mitochondrial ClpP in complex with TR89 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ypa
TitleHuman mitochondrial ClpP in complex with TR89
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / Mitochondria / Caseinolytic Protease P / activator / antitumor
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / 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 / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / 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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsLi, Q.-N. / Sun, H.-Y. / Xiao, Y.-B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human mitochondrial ClpP in complex with TR89
Authors: Li, Q.-N. / Sun, H.-Y. / Xiao, Y.-B.
History
DepositionMar 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,52614
Polymers170,2687
Non-polymers3,2587
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.882, 152.424, 104.446
Angle α, β, γ (deg.)90.000, 118.050, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 58 and (name N or name...
d_2ens_1(chain "B" and ((resid 58 and (name N or name...
d_3ens_1(chain "C" and ((resid 58 and (name N or name...
d_4ens_1(chain "D" and ((resid 58 and (name N or name...
d_5ens_1(chain "E" and (resid 58 through 63 or (resid 70...
d_6ens_1(chain "F" and (resid 58 through 72 or (resid 73...
d_7ens_1(chain "G" and (resid 58 through 111 or (resid 112...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 58 - 247 / Label seq-ID: 4 - 193

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG

NCS oper:
IDCodeMatrixVector
1given(-0.890272103748, -0.103655263338, 0.443476231235), (-0.102560713924, -0.903112224065, -0.416976750795), (0.44373064042, -0.416706008028, 0.793384661829)2.86615115786, 62.0367405263, 13.4097433699
2given(-0.930984085389, 0.227990057715, 0.285112550294), (0.23623277713, -0.219190818399, 0.946651710049), (0.278321231245, 0.948670606013, 0.150204439101)14.7315406425, 18.3885938151, 61.4520966748
3given(-0.978498601379, 0.18455542801, 0.0920857268651), (0.189171964105, 0.625143990847, 0.757237716114), (0.0821854920104, 0.758376083945, -0.646615233506)21.6727103631, 39.7629238222, 90.4098442939
4given(-0.978576292836, -0.18609309503, 0.0880783689778), (-0.186674331121, 0.621534353402, -0.760820439816), (0.0868396982963, -0.760962816124, -0.642957587463)15.6476820391, 100.640001519, 65.4728663614
5given(-0.891418518492, 0.104231629278, 0.441031509473), (0.105338282498, -0.898878494836, 0.425348442764), (0.440768500611, 0.425620980427, 0.790297355361)6.31595676486, 28.2210611618, 27.2706042351
6given(-0.929548259574, -0.230309187265, 0.287919626605), (-0.236386499249, -0.227017685317, -0.944766846119), (0.282951331674, -0.946266690112, 0.156581911756)6.89142771343, 94.2157705572, 30.3342625228

-
Components

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


Mass: 24324.004 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical
ChemComp-A1LZN / (6~{R})-2-[[3,5-bis(fluoranyl)phenyl]methyl]-6-(hydroxymethyl)-5-[[4-(trifluoromethyl)phenyl]methyl]-7,8-dihydro-6~{H}-pyrazolo[1,5-a][1,4]diazepin-4-one


Mass: 465.416 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C23H20F5N3O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 M sodium acetate ph 6.2, 8% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.67→46.09 Å / Num. obs: 55979 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 35.76 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1995 / Rpim(I) all: 0.08187 / Rrim(I) all: 0.2159 / Net I/σ(I): 8.52
Reflection shellResolution: 2.67→2.765 Å / Num. unique obs: 5582 / CC1/2: 0.755

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→46.09 Å / SU ML: 0.359 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1999 3.57 %
Rwork0.2146 53980 -
obs0.2161 55979 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.51 Å2
Refinement stepCycle: LAST / Resolution: 2.67→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9542 0 231 0 9773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00869951
X-RAY DIFFRACTIONf_angle_d1.054813505
X-RAY DIFFRACTIONf_chiral_restr0.05791569
X-RAY DIFFRACTIONf_plane_restr0.00811677
X-RAY DIFFRACTIONf_dihedral_angle_d17.86393636
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.401671955867
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.458754506963
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.40272200254
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.506982526914
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.497983376674
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.459757727512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.730.32511400.28223785X-RAY DIFFRACTION98.67
2.73-2.810.35821420.27223841X-RAY DIFFRACTION100
2.81-2.890.32411440.26423868X-RAY DIFFRACTION100
2.89-2.980.30861440.25393879X-RAY DIFFRACTION99.98
2.98-3.090.28651400.24463814X-RAY DIFFRACTION100
3.09-3.220.32551420.23383823X-RAY DIFFRACTION99.97
3.22-3.360.28761440.22143896X-RAY DIFFRACTION100
3.36-3.540.2471420.22483839X-RAY DIFFRACTION99.97
3.54-3.760.29691430.21993855X-RAY DIFFRACTION99.97
3.76-4.050.23091430.18973872X-RAY DIFFRACTION100
4.05-4.460.19281430.17673852X-RAY DIFFRACTION99.97
4.46-5.10.23771440.17863869X-RAY DIFFRACTION99.98
5.1-6.430.25061430.2193891X-RAY DIFFRACTION99.95
6.43-46.090.20051450.19383896X-RAY DIFFRACTION99.12
Refinement TLS params.Method: refined / Origin x: 22.2795220851 Å / Origin y: 49.0287095996 Å / Origin z: 50.5957462836 Å
111213212223313233
T0.220438428175 Å20.00307577157191 Å20.00453693893916 Å2-0.257242297636 Å20.00126332370957 Å2--0.219990281057 Å2
L0.111878112159 °20.0613670384857 °2-0.029914568242 °2-0.261278054518 °20.0177148540895 °2--0.0784861627513 °2
S-0.0159631863288 Å °0.0143135675911 Å °-0.00186099320105 Å °0.0106659427865 Å °0.0107847257428 Å °0.0415193121535 Å °0.0212044078612 Å °-0.016959517396 Å °0.00316680588876 Å °
Refinement TLS groupSelection details: all

+
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