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- PDB-8b9u: Structure of ClpC1 NTD from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8b9u
TitleStructure of ClpC1 NTD from Mycobacterium tuberculosis
Components
  • (MLE)V(MAA)(E9M)G
  • ATP-dependent Clp protease ATP-binding subunit ClpC1
KeywordsCHAPERONE / ligand bound state
Function / homology
Function and homology information


protein folding chaperone / peptidoglycan-based cell wall / protein homodimerization activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. ...UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Nonomuraea sp. MJM5123 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMeinhart, A. / Hoi, D.M. / Clausen, T.
Funding supportEuropean Union, Austria, 2items
OrganizationGrant numberCountry
European Research Council (ERC)AdG 694978European Union
Vienna Science and Technology Fund (WWTF)852936 Austria
CitationJournal: Cell / Year: 2023
Title: Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival.
Authors: Hoi, D.M. / Junker, S. / Junk, L. / Schwechel, K. / Fischel, K. / Podlesainski, D. / Hawkins, P.M.E. / van Geelen, L. / Kaschani, F. / Leodolter, J. / Morreale, F.E. / Kleine, S. / Guha, S. ...Authors: Hoi, D.M. / Junker, S. / Junk, L. / Schwechel, K. / Fischel, K. / Podlesainski, D. / Hawkins, P.M.E. / van Geelen, L. / Kaschani, F. / Leodolter, J. / Morreale, F.E. / Kleine, S. / Guha, S. / Rumpel, K. / Schmiedel, V.M. / Weinstabl, H. / Meinhart, A. / Payne, R.J. / Kaiser, M. / Hartl, M. / Boehmelt, G. / Kazmaier, U. / Kalscheuer, R. / Clausen, T.
History
DepositionOct 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC1
B: ATP-dependent Clp protease ATP-binding subunit ClpC1
C: (MLE)V(MAA)(E9M)G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,58710
Polymers32,2653
Non-polymers3227
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-15 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.440, 57.440, 174.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ATP-dependent Clp protease ATP-binding subunit ClpC1


Mass: 15839.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9
#2: Protein/peptide (MLE)V(MAA)(E9M)G


Mass: 586.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nonomuraea sp. MJM5123 (bacteria)
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10 mM Tris-HCl pH 7.5 and 3.1 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54789 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54789 Å / Relative weight: 1
ReflectionResolution: 2.25→99 Å / Num. obs: 16532 / % possible obs: 98.9 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rrim(I) all: 0.089 / Net I/σ(I): 19.7
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 10.5 % / Num. unique obs: 1084 / CC1/2: 0.933 / Rrim(I) all: 0.653 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDB

3wdb


Resolution: 2.25→47.84 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 824 5 %
Rwork0.2123 --
obs0.2141 16475 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 24 110 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.438
X-RAY DIFFRACTIONf_dihedral_angle_d16.841856
X-RAY DIFFRACTIONf_chiral_restr0.035358
X-RAY DIFFRACTIONf_plane_restr0.003398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.390.48261290.41442465X-RAY DIFFRACTION95
2.39-2.570.31171350.27552554X-RAY DIFFRACTION100
2.57-2.830.29861360.22082595X-RAY DIFFRACTION100
2.83-3.240.2561380.22712608X-RAY DIFFRACTION100
3.24-4.090.20341390.18442639X-RAY DIFFRACTION100
4.09-47.840.21481470.17592790X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0209-0.43590.99474.2174-0.41885.68220.28460.0822-0.3499-0.1849-0.23460.68820.3619-0.70440.13350.33180.0052-0.06170.3313-0.07050.4059-37.3858-7.8389-24.7589
20.75670.0887-0.19463.8213-0.22293.05360.13080.3903-0.0607-0.6601-0.22760.5579-0.4748-0.60620.14770.5080.2362-0.14680.4439-0.0660.3633-36.38614.8373-31.3142
33.43242.08450.63444.06220.78345.39270.2071-0.0075-0.325-0.1599-0.136-0.43810.38390.5018-0.15610.27810.06210.0060.2661-0.03510.3119-19.5663-0.0416-8.6888
41.99810.2686-0.14034.62951.10644.26910.1895-0.36990.19490.2625-0.0501-0.3884-0.27580.4039-0.10320.2582-0.1113-0.00550.3421-0.03660.3014-16.344811.1267-0.0541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 81)
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 142 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 81 )
4X-RAY DIFFRACTION4chain 'B' and (resid 82 through 144)

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