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- PDB-9q3z: Structure of the ClpC1-N-terminal Domain of M. tuberculosis compl... -

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Basic information

Entry
Database: PDB / ID: 9q3z
TitleStructure of the ClpC1-N-terminal Domain of M. tuberculosis complexed with P-Arginine bound to site no. 1
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC1
KeywordsCHAPERONE / ClpC1 ATPase / Rufomycin / Antibiotic / ClpC1-NTD-complex / CHAPERONE-ANTIBIOTIC complex
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 repeat (R) N-terminal domain / Clp repeat (R) domain profile. / Clp, repeat (R) domain ...UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / Clp repeat (R) N-terminal domain / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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
phospho-arginine / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsAbad-Zapatero, C. / Ratia, K.M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Other governmentS2014-202 Japan
Other governmentH2018-202 Japan
Citation
Journal: To Be Published
Title: Isolation, Structural Characterization, and Biological Activity of Novel Terpenoid Natural Products Active Against Mycobacterium tuberculosis.
Authors: Abad-Zapatero, C. / Ratia, K.M. / Lee, H. / Franzblau, S.G. / Shetye, G. / Kaneko, T.
#1: Journal: Acs Infect Dis. / Year: 2019
Title: High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads.
Authors: Wolf, N.M. / Lee, H. / Choules, M.P. / Pauli, G.F. / Phansalkar, R. / Anderson, J.R. / Gao, W. / Ren, J. / Santarsiero, B.D. / Lee, H. / Cheng, J. / Jin, Y.Y. / Ho, N.A. / Duc, N.M. / Suh, J. ...Authors: Wolf, N.M. / Lee, H. / Choules, M.P. / Pauli, G.F. / Phansalkar, R. / Anderson, J.R. / Gao, W. / Ren, J. / Santarsiero, B.D. / Lee, H. / Cheng, J. / Jin, Y.Y. / Ho, N.A. / Duc, N.M. / Suh, J.W. / Abad-Zapatero, C. / Cho, S.
#2: Journal: J.Nat.Prod. / Year: 2025
Title: Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues.
Authors: Zhou, B. / Shetye, G. / Klein, L.L. / Wolf, N.M. / Lee, H. / McAlpine, J.B. / Harris, G. / Chen, S.N. / Suh, J.W. / Cho, S.H. / Franzblau, S.G. / Abad-Zapatero, C. / Pauli, G.F.
History
DepositionAug 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7832
Polymers17,5291
Non-polymers2541
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, The ClpC1-N-terminal Domain complexed with a phosphorylated Arginine residue. P-Arg is a tag that signals proteins for degradation in the Proteolytic Machinery ClpC1/P1/P2.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.370, 60.330, 36.140
Angle α, β, γ (deg.)90.000, 113.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 17529.131 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9
#2: Chemical ChemComp-RPI / phospho-arginine


Type: L-peptide linking / Mass: 254.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 25% PEG 3350, 1:1 ratio of reservoir to Drop, 2 mM P-Arg
PH range: 8.5 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2021 / Details: Diamond
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.53→60.33 Å / Num. obs: 20318 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 13.11 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.047 / Rrim(I) all: 0.067 / Rsym value: 0.051 / Net I/σ(I): 13.2
Reflection shellResolution: 1.53→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 991 / CC1/2: 0.964 / Rpim(I) all: 0.157 / Rrim(I) all: 0.24 / Χ2: 0.79 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→33.06 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1875 1115 5.5 %
Rwork0.1591 19175 -
obs0.1606 20290 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.93 Å2
Refinement stepCycle: LAST / Resolution: 1.53→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 0 144 1334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791203
X-RAY DIFFRACTIONf_angle_d1.06861620
X-RAY DIFFRACTIONf_chiral_restr0.0538188
X-RAY DIFFRACTIONf_plane_restr0.0161209
X-RAY DIFFRACTIONf_dihedral_angle_d7.1414170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.60.21651170.17952358X-RAY DIFFRACTION96.83
1.6-1.680.19661360.17282379X-RAY DIFFRACTION98.2
1.68-1.780.21451500.16152371X-RAY DIFFRACTION98.44
1.78-1.920.1961440.15742401X-RAY DIFFRACTION98.45
1.92-2.120.20621340.15662400X-RAY DIFFRACTION99.06
2.12-2.420.18431410.14882421X-RAY DIFFRACTION99.19
2.42-3.050.19491380.15792415X-RAY DIFFRACTION99.53
3.05-33.060.16721550.162430X-RAY DIFFRACTION98.51

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