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- PDB-7vp9: Crystal structure of human ClpP in complex with ZG111 -

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Basic information

Entry
Database: PDB / ID: 7vp9
TitleCrystal structure of human ClpP in complex with ZG111
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / mitochondrial protease
Function / homology
Function and homology information


membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix ...membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / 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
Chem-7SR / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsWang, P.Y. / Gan, J.H. / Yang, C.-G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22037007 China
National Natural Science Foundation of China (NSFC)21725801 China
National Natural Science Foundation of China (NSFC)22107109 China
CitationJournal: Cell Chem Biol / Year: 2022
Title: Aberrant human ClpP activation disturbs mitochondrial proteome homeostasis to suppress pancreatic ductal adenocarcinoma.
Authors: Wang, P. / Zhang, T. / Wang, X. / Xiao, H. / Li, H. / Zhou, L.L. / Yang, T. / Wei, B. / Zhu, Z. / Zhou, L. / Yang, S. / Lu, X. / Zhang, Y. / Huang, Y. / Gan, J. / Yang, C.G.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: ATP-dependent Clp protease proteolytic subunit, mitochondrial
I: ATP-dependent Clp protease proteolytic subunit, mitochondrial
J: ATP-dependent Clp protease proteolytic subunit, mitochondrial
K: ATP-dependent Clp protease proteolytic subunit, mitochondrial
L: ATP-dependent Clp protease proteolytic subunit, mitochondrial
M: ATP-dependent Clp protease proteolytic subunit, mitochondrial
N: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,08442
Polymers338,65914
Non-polymers8,42528
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Two heptameric monocyclic assemble into a tetradecamer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52290 Å2
ΔGint-325 kcal/mol
Surface area82200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.806, 97.408, 146.686
Angle α, β, γ (deg.)90.000, 90.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 59 through 60 or (resid 61...
21(chain B and (resid 59 through 60 or (resid 61...
31(chain C and (resid 59 through 111 or (resid 112...
41(chain D and (resid 59 through 60 or (resid 61...
51(chain E and (resid 59 through 60 or (resid 61...
61(chain F and (resid 59 through 60 or (resid 61...
71(chain G and (resid 59 through 60 or (resid 61...
81(chain H and (resid 59 through 60 or (resid 61...
91(chain I and (resid 59 through 60 or (resid 61...
101(chain J and (resid 59 through 60 or (resid 61...
111(chain K and (resid 59 through 60 or (resid 61...
121(chain L and (resid 59 through 60 or (resid 61...
131(chain M and (resid 59 through 60 or (resid 61...
141(chain N and (resid 59 through 60 or (resid 61...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPROPRO(chain A and (resid 59 through 60 or (resid 61...AA59 - 603 - 4
12ILEILEILEILE(chain A and (resid 59 through 60 or (resid 61...AA615
13LEULEUPROPRO(chain A and (resid 59 through 60 or (resid 61...AA58 - 2492 - 193
14LEULEUPROPRO(chain A and (resid 59 through 60 or (resid 61...AA58 - 2492 - 193
15LEULEUPROPRO(chain A and (resid 59 through 60 or (resid 61...AA58 - 2492 - 193
16LEULEUPROPRO(chain A and (resid 59 through 60 or (resid 61...AA58 - 2492 - 193
21ILEILEPROPRO(chain B and (resid 59 through 60 or (resid 61...BB59 - 603 - 4
22ILEILEILEILE(chain B and (resid 59 through 60 or (resid 61...BB615
23LEULEUPROPRO(chain B and (resid 59 through 60 or (resid 61...BB58 - 2492 - 193
24LEULEUPROPRO(chain B and (resid 59 through 60 or (resid 61...BB58 - 2492 - 193
25LEULEUPROPRO(chain B and (resid 59 through 60 or (resid 61...BB58 - 2492 - 193
26LEULEUPROPRO(chain B and (resid 59 through 60 or (resid 61...BB58 - 2492 - 193
31ILEILEASNASN(chain C and (resid 59 through 111 or (resid 112...CC59 - 1113 - 55
32LYSLYSLYSLYS(chain C and (resid 59 through 111 or (resid 112...CC112 - 11356 - 57
33ILEILEPROPRO(chain C and (resid 59 through 111 or (resid 112...CC59 - 2493 - 193
34ILEILEPROPRO(chain C and (resid 59 through 111 or (resid 112...CC59 - 2493 - 193
35ILEILEPROPRO(chain C and (resid 59 through 111 or (resid 112...CC59 - 2493 - 193
36ILEILEPROPRO(chain C and (resid 59 through 111 or (resid 112...CC59 - 2493 - 193
41ILEILEPROPRO(chain D and (resid 59 through 60 or (resid 61...DD59 - 603 - 4
42ILEILEILEILE(chain D and (resid 59 through 60 or (resid 61...DD615
43LEULEUPROPRO(chain D and (resid 59 through 60 or (resid 61...DD58 - 2482 - 192
44LEULEUPROPRO(chain D and (resid 59 through 60 or (resid 61...DD58 - 2482 - 192
45LEULEUPROPRO(chain D and (resid 59 through 60 or (resid 61...DD58 - 2482 - 192
46LEULEUPROPRO(chain D and (resid 59 through 60 or (resid 61...DD58 - 2482 - 192
51ILEILEPROPRO(chain E and (resid 59 through 60 or (resid 61...EE59 - 603 - 4
52ILEILEILEILE(chain E and (resid 59 through 60 or (resid 61...EE615
53LEULEUPROPRO(chain E and (resid 59 through 60 or (resid 61...EE58 - 2492 - 193
54LEULEUPROPRO(chain E and (resid 59 through 60 or (resid 61...EE58 - 2492 - 193
55LEULEUPROPRO(chain E and (resid 59 through 60 or (resid 61...EE58 - 2492 - 193
56LEULEUPROPRO(chain E and (resid 59 through 60 or (resid 61...EE58 - 2492 - 193
61ILEILEPROPRO(chain F and (resid 59 through 60 or (resid 61...FF59 - 603 - 4
62ILEILEILEILE(chain F and (resid 59 through 60 or (resid 61...FF615
63PROPROPROPRO(chain F and (resid 59 through 60 or (resid 61...FF57 - 2491 - 193
64PROPROPROPRO(chain F and (resid 59 through 60 or (resid 61...FF57 - 2491 - 193
65PROPROPROPRO(chain F and (resid 59 through 60 or (resid 61...FF57 - 2491 - 193
66PROPROPROPRO(chain F and (resid 59 through 60 or (resid 61...FF57 - 2491 - 193
71ILEILEPROPRO(chain G and (resid 59 through 60 or (resid 61...GG59 - 603 - 4
72ILEILEILEILE(chain G and (resid 59 through 60 or (resid 61...GG615
73LEULEUPROPRO(chain G and (resid 59 through 60 or (resid 61...GG58 - 2492 - 193
74LEULEUPROPRO(chain G and (resid 59 through 60 or (resid 61...GG58 - 2492 - 193
75LEULEUPROPRO(chain G and (resid 59 through 60 or (resid 61...GG58 - 2492 - 193
76LEULEUPROPRO(chain G and (resid 59 through 60 or (resid 61...GG58 - 2492 - 193
81ILEILEPROPRO(chain H and (resid 59 through 60 or (resid 61...HH59 - 603 - 4
82ILEILEILEILE(chain H and (resid 59 through 60 or (resid 61...HH615
83LEULEUPROPRO(chain H and (resid 59 through 60 or (resid 61...HH58 - 2492 - 193
84LEULEUPROPRO(chain H and (resid 59 through 60 or (resid 61...HH58 - 2492 - 193
85LEULEUPROPRO(chain H and (resid 59 through 60 or (resid 61...HH58 - 2492 - 193
86LEULEUPROPRO(chain H and (resid 59 through 60 or (resid 61...HH58 - 2492 - 193
91ILEILEPROPRO(chain I and (resid 59 through 60 or (resid 61...II59 - 603 - 4
92ILEILEILEILE(chain I and (resid 59 through 60 or (resid 61...II615
93PROPROPROPRO(chain I and (resid 59 through 60 or (resid 61...II57 - 2491 - 193
94PROPROPROPRO(chain I and (resid 59 through 60 or (resid 61...II57 - 2491 - 193
95PROPROPROPRO(chain I and (resid 59 through 60 or (resid 61...II57 - 2491 - 193
96PROPROPROPRO(chain I and (resid 59 through 60 or (resid 61...II57 - 2491 - 193
101ILEILEPROPRO(chain J and (resid 59 through 60 or (resid 61...JJ59 - 603 - 4
102ILEILEILEILE(chain J and (resid 59 through 60 or (resid 61...JJ615
103PROPROPROPRO(chain J and (resid 59 through 60 or (resid 61...JJ57 - 2491 - 193
104PROPROPROPRO(chain J and (resid 59 through 60 or (resid 61...JJ57 - 2491 - 193
105PROPROPROPRO(chain J and (resid 59 through 60 or (resid 61...JJ57 - 2491 - 193
106PROPROPROPRO(chain J and (resid 59 through 60 or (resid 61...JJ57 - 2491 - 193
111ILEILEPROPRO(chain K and (resid 59 through 60 or (resid 61...KK59 - 603 - 4
112ILEILEILEILE(chain K and (resid 59 through 60 or (resid 61...KK615
113PROPROPROPRO(chain K and (resid 59 through 60 or (resid 61...KK57 - 2491 - 193
114PROPROPROPRO(chain K and (resid 59 through 60 or (resid 61...KK57 - 2491 - 193
115PROPROPROPRO(chain K and (resid 59 through 60 or (resid 61...KK57 - 2491 - 193
116PROPROPROPRO(chain K and (resid 59 through 60 or (resid 61...KK57 - 2491 - 193
121ILEILEPROPRO(chain L and (resid 59 through 60 or (resid 61...LL59 - 603 - 4
122ILEILEILEILE(chain L and (resid 59 through 60 or (resid 61...LL615
123PROPROPROPRO(chain L and (resid 59 through 60 or (resid 61...LL57 - 2491 - 193
124PROPROPROPRO(chain L and (resid 59 through 60 or (resid 61...LL57 - 2491 - 193
125PROPROPROPRO(chain L and (resid 59 through 60 or (resid 61...LL57 - 2491 - 193
126PROPROPROPRO(chain L and (resid 59 through 60 or (resid 61...LL57 - 2491 - 193
131ILEILEPROPRO(chain M and (resid 59 through 60 or (resid 61...MM59 - 603 - 4
132ILEILEILEILE(chain M and (resid 59 through 60 or (resid 61...MM615
133LEULEUPROPRO(chain M and (resid 59 through 60 or (resid 61...MM58 - 2482 - 192
134LEULEUPROPRO(chain M and (resid 59 through 60 or (resid 61...MM58 - 2482 - 192
135LEULEUPROPRO(chain M and (resid 59 through 60 or (resid 61...MM58 - 2482 - 192
136LEULEUPROPRO(chain M and (resid 59 through 60 or (resid 61...MM58 - 2482 - 192
141ILEILEPROPRO(chain N and (resid 59 through 60 or (resid 61...NN59 - 603 - 4
142ILEILEILEILE(chain N and (resid 59 through 60 or (resid 61...NN615
143LEULEUPROPRO(chain N and (resid 59 through 60 or (resid 61...NN58 - 2482 - 192
144LEULEUPROPRO(chain N and (resid 59 through 60 or (resid 61...NN58 - 2482 - 192
145LEULEUPROPRO(chain N and (resid 59 through 60 or (resid 61...NN58 - 2482 - 192
146LEULEUPROPRO(chain N and (resid 59 through 60 or (resid 61...NN58 - 2482 - 192

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Components

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


Mass: 24189.912 Da / Num. of mol.: 14
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-7SR / (6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide


Mass: 577.512 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C30H33BrN4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium bromide, 20% (w/v) polyethylene glycol 3350
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→28.838 Å / Num. obs: 90730 / % possible obs: 95.18 % / Redundancy: 3.8 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.095 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.642.50.29884160.5330.2040.3640.2989.3
2.64-2.752.60.28684530.5620.1920.3470.32789.5
2.75-2.8730.26888940.6980.1680.3190.34693.8
2.87-3.023.30.22190180.8320.1330.260.41295.4
3.02-3.213.50.18190750.9020.1060.2110.46496.1
3.21-3.463.80.15392140.930.0860.1770.56397
3.46-3.814.30.1193010.9120.0590.1260.71498.2
3.81-4.364.30.08393060.9890.0450.0950.8897.9
4.36-5.484.80.06594480.9930.0330.0740.94298.9
5.48-305.40.05496050.9970.0250.0591.18998.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TG6

1tg6


Resolution: 2.552→28.838 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 4637 5.11 %
Rwork0.2019 --
obs0.2034 90673 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.51 Å2 / Biso mean: 62.8249 Å2 / Biso min: 19.14 Å2
Refinement stepCycle: final / Resolution: 2.552→28.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18668 0 546 55 19269
Biso mean--70.46 46.81 -
Num. residues----2439
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11117X-RAY DIFFRACTION14.062TORSIONAL
12B11117X-RAY DIFFRACTION14.062TORSIONAL
13C11117X-RAY DIFFRACTION14.062TORSIONAL
14D11117X-RAY DIFFRACTION14.062TORSIONAL
15E11117X-RAY DIFFRACTION14.062TORSIONAL
16F11117X-RAY DIFFRACTION14.062TORSIONAL
17G11117X-RAY DIFFRACTION14.062TORSIONAL
18H11117X-RAY DIFFRACTION14.062TORSIONAL
19I11117X-RAY DIFFRACTION14.062TORSIONAL
110J11117X-RAY DIFFRACTION14.062TORSIONAL
111K11117X-RAY DIFFRACTION14.062TORSIONAL
112L11117X-RAY DIFFRACTION14.062TORSIONAL
113M11117X-RAY DIFFRACTION14.062TORSIONAL
114N11117X-RAY DIFFRACTION14.062TORSIONAL
LS refinement shellResolution: 2.5516→2.5806 Å
RfactorNum. reflection
Rfree0.3534 151
Rwork0.3059 -
obs-2422
Refinement TLS params.Method: refined / Origin x: 24.6254 Å / Origin y: -8.8888 Å / Origin z: 36.0402 Å
111213212223313233
T0.2154 Å20.0226 Å20.0222 Å2-0.2418 Å20.0238 Å2--0.1413 Å2
L0.298 °2-0.0111 °20.1728 °2-0.391 °20.0514 °2--0.2749 °2
S-0.0077 Å °-0.1622 Å °-0.0206 Å °0.1703 Å °0.0343 Å °-0.0046 Å °0.0122 Å °-0.0991 Å °0.0015 Å °
Refinement TLS groupSelection details: all

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