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- PDB-6dfk: Crystal structure of the 11S subunit of the Plasmodium falciparum... -

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Basic information

Entry
Database: PDB / ID: 6dfk
TitleCrystal structure of the 11S subunit of the Plasmodium falciparum proteasome, PA28
ComponentsSubunit of proteaseome activator complex,putative
KeywordsPROTEIN BINDING / 11S proteasome subunit / 11S regulatory particle / PA28 / REG / proteasome activator / hydrolase activator
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / proteasome activator complex ...Cross-presentation of soluble exogenous antigens (endosomes) / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / proteasome activator complex / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / nucleoplasm / cytoplasm
Similarity search - Function
Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit
Similarity search - Domain/homology
Proteasome activator 28 subunit beta, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsXie, S.C. / Metcalfe, R.D. / Gillett, D.L. / Tilley, L. / Griffin, M.D.W.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
Global Health Innovative Technology Fund
GSK Tres Cantos Open Lab Foundation
CitationJournal: Nat Microbiol / Year: 2019
Title: The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis.
Authors: Stanley C Xie / Riley D Metcalfe / Eric Hanssen / Tuo Yang / David L Gillett / Andrew P Leis / Craig J Morton / Michael J Kuiper / Michael W Parker / Natalie J Spillman / Wilson Wong / ...Authors: Stanley C Xie / Riley D Metcalfe / Eric Hanssen / Tuo Yang / David L Gillett / Andrew P Leis / Craig J Morton / Michael J Kuiper / Michael W Parker / Natalie J Spillman / Wilson Wong / Christopher Tsu / Lawrence R Dick / Michael D W Griffin / Leann Tilley /
Abstract: The activity of the proteasome 20S catalytic core is regulated by protein complexes that bind to one or both ends. The PA28 regulator stimulates 20S proteasome peptidase activity in vitro, but its ...The activity of the proteasome 20S catalytic core is regulated by protein complexes that bind to one or both ends. The PA28 regulator stimulates 20S proteasome peptidase activity in vitro, but its role in vivo remains unclear. Here, we show that genetic deletion of the PA28 regulator from Plasmodium falciparum (Pf) renders malaria parasites more sensitive to the antimalarial drug dihydroartemisinin, indicating that PA28 may play a role in protection against proteotoxic stress. The crystal structure of PfPA28 reveals a bell-shaped molecule with an inner pore that has a strong segregation of charges. Small-angle X-ray scattering shows that disordered loops, which are not resolved in the crystal structure, extend from the PfPA28 heptamer and surround the pore. Using single particle cryo-electron microscopy, we solved the structure of Pf20S in complex with one and two regulatory PfPA28 caps at resolutions of 3.9 and 3.8 Å, respectively. PfPA28 binds Pf20S asymmetrically, strongly engaging subunits on only one side of the core. PfPA28 undergoes rigid body motions relative to Pf20S. Molecular dynamics simulations support conformational flexibility and a leaky interface. We propose lateral transfer of short peptides through the dynamic interface as a mechanism facilitating the release of proteasome degradation products.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / 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 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subunit of proteaseome activator complex,putative
B: Subunit of proteaseome activator complex,putative
C: Subunit of proteaseome activator complex,putative
D: Subunit of proteaseome activator complex,putative
E: Subunit of proteaseome activator complex,putative
F: Subunit of proteaseome activator complex,putative
G: Subunit of proteaseome activator complex,putative
H: Subunit of proteaseome activator complex,putative
I: Subunit of proteaseome activator complex,putative
J: Subunit of proteaseome activator complex,putative
K: Subunit of proteaseome activator complex,putative
L: Subunit of proteaseome activator complex,putative
M: Subunit of proteaseome activator complex,putative
N: Subunit of proteaseome activator complex,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,06574
Polymers465,30214
Non-polymers5,76460
Water0
1
A: Subunit of proteaseome activator complex,putative
B: Subunit of proteaseome activator complex,putative
C: Subunit of proteaseome activator complex,putative
D: Subunit of proteaseome activator complex,putative
E: Subunit of proteaseome activator complex,putative
F: Subunit of proteaseome activator complex,putative
G: Subunit of proteaseome activator complex,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,53337
Polymers232,6517
Non-polymers2,88230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43800 Å2
ΔGint-640 kcal/mol
Surface area67770 Å2
MethodPISA
2
H: Subunit of proteaseome activator complex,putative
I: Subunit of proteaseome activator complex,putative
J: Subunit of proteaseome activator complex,putative
K: Subunit of proteaseome activator complex,putative
L: Subunit of proteaseome activator complex,putative
M: Subunit of proteaseome activator complex,putative
N: Subunit of proteaseome activator complex,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,53337
Polymers232,6517
Non-polymers2,88230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44790 Å2
ΔGint-640 kcal/mol
Surface area67540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.485, 166.485, 399.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Subunit of proteaseome activator complex,putative


Mass: 33235.824 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_0907700 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I374
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: SO4

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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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20 mM HEPES, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→48.89 Å / Num. obs: 116975 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 60.6 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.131 / Rrim(I) all: 0.305 / Net I/σ(I): 7.5
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5711 / CC1/2: 0.513 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVO

1avo


Resolution: 3.1→48.89 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 22.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 3534 3.02 %Random; Thin shells
Rwork0.1817 ---
obs0.183 116839 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26198 0 300 0 26498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326942
X-RAY DIFFRACTIONf_angle_d0.63636381
X-RAY DIFFRACTIONf_dihedral_angle_d1.84616405
X-RAY DIFFRACTIONf_chiral_restr0.0453963
X-RAY DIFFRACTIONf_plane_restr0.0034545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.21080.31742270.29911348X-RAY DIFFRACTION100
3.2108-3.33930.31085340.26211020X-RAY DIFFRACTION100
3.3393-3.49120.26711930.23711333X-RAY DIFFRACTION100
3.4912-3.67530.28693580.217311225X-RAY DIFFRACTION100
3.6753-3.90540.23994030.185911185X-RAY DIFFRACTION100
3.9054-4.20680.19024490.149711179X-RAY DIFFRACTION100
4.2068-4.62990.18112640.136611437X-RAY DIFFRACTION100
4.6299-5.29910.1923620.141311326X-RAY DIFFRACTION100
5.2991-6.67370.22133660.188811479X-RAY DIFFRACTION100
6.6737-48.89630.20813780.169511773X-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)
10.577-0.22610.18231.7646-0.33821.57250.1433-0.1079-0.13770.1671-0.028-0.04710.3541-0.0557-0.08930.5749-0.1187-0.03350.34020.05590.3769-69.24425.266316.7894
20.8044-0.63860.1012.94250.07791.29590.0473-0.0281-0.0859-0.088-0.01970.10950.1952-0.1856-0.06080.3818-0.1402-0.03530.37310.01610.278-72.398433.4304-4.7258
31.2078-0.4785-0.53811.76770.451.4733-0.0578-0.019-0.0345-0.06940.1104-0.07940.05440.1669-0.08310.3565-0.0835-0.06050.42720.0190.2811-62.432351.0072-15.8381
41.8457-0.2905-0.74961.63040.71872.4639-0.15790.1880.15650.21710.135-0.0834-0.07530.12530.00460.4298-0.1416-0.09580.38530.05230.4073-51.803268.0786-5.3335
51.91280.2708-0.58440.76820.03511.750.0369-0.2534-0.09020.3293-0.0484-0.1825-0.25340.425-0.03160.6232-0.1695-0.20630.46720.03710.5482-41.593269.001916.1023
64.31120.788-0.63630.6491-0.5731.27310.1497-0.3121-0.00050.4095-0.1323-0.1698-0.19330.2365-0.03550.8859-0.1276-0.220.4688-0.00670.4622-49.164356.374234.3795
73.2273-0.27920.88741.1976-0.33721.09950.2332-0.1299-0.10930.2816-0.1707-0.26530.03860.0687-0.08960.7812-0.0353-0.08820.44890.08860.3726-58.198435.381834.4325
81.0274-0.4002-0.04811.87960.87641.237-0.0257-0.05430.1217-0.04260.0227-0.0728-0.10130.05440.00680.38-0.0865-0.01590.45180.05720.2797-77.412170.6099-31.9352
91.02890.71260.21762.35160.76271.44230.02940.1342-0.04040.07230.0358-0.0214-0.01710.1341-0.09380.2615-0.01030.00610.55830.07680.3087-64.075565.3467-49.6097
101.31310.95490.22141.39750.03260.9126-0.05920.4920.0242-0.110.1421-0.0093-0.08260.2436-0.08530.33440.04810.05190.72910.03590.3273-67.853767.2277-72.8265
111.60060.735-0.04411.1848-0.45631.0399-0.03880.44280.1435-0.06760.1380.1082-0.08910.0333-0.08930.4180.08040.01250.75720.00850.3523-87.408968.2105-83.1168
121.39430.5177-0.34131.5255-0.96451.29660.00210.31190.105-0.06440.0636-0.04530.0079-0.103-0.05840.28250.0299-0.03260.6515-0.00490.3971-108.567767.6756-73.2314
131.2784-0.67070.18651.7967-0.24830.7343-0.05950.02840.12590.1554-0.0024-0.0042-0.1622-0.2080.00140.28140.0330.00750.5934-0.04240.3854-114.607173.4597-51.1607
141.4348-1.01160.49632.91180.07441.27050.0269-0.23180.06970.0902-0.02920.0509-0.0315-0.1859-0.01410.3238-0.06340.03990.48140.00340.2592-100.610669.9009-32.8398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 269)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 270)
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 270)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 269)
5X-RAY DIFFRACTION5(chain 'E' and resid 7 through 270)
6X-RAY DIFFRACTION6(chain 'F' and resid 8 through 269)
7X-RAY DIFFRACTION7(chain 'G' and resid 6 through 269)
8X-RAY DIFFRACTION8(chain 'H' and resid 6 through 269)
9X-RAY DIFFRACTION9(chain 'I' and resid 5 through 270)
10X-RAY DIFFRACTION10(chain 'J' and resid 6 through 270)
11X-RAY DIFFRACTION11(chain 'K' and resid 0 through 270)
12X-RAY DIFFRACTION12(chain 'L' and resid 5 through 269)
13X-RAY DIFFRACTION13(chain 'M' and resid 6 through 270)
14X-RAY DIFFRACTION14(chain 'N' and resid 6 through 269)

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