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- EMDB-0967: AAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound -

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Basic information

Entry
Database: EMDB / ID: EMD-0967
TitleAAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound
Map data
Sample
  • Organelle or cellular component: AAA+ ATPase, chaperone
    • Protein or peptide: ATP-dependent Clp protease, ATP-binding subunit
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsAAA+ ATPase / chaperone / ClpL / Streptococcus pneumoniae
Function / homology
Function and homology information


peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding
Similarity search - Function
UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) ...UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / 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
ATP-dependent Clp protease, ATP-binding subunit
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria) / Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKim G / Seong-Gyu L
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2B6004367 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1A5A1014560 Korea, Republic Of
Rural Development AdministrationPJ01367602 Korea, Republic Of
CitationJournal: FASEB J / Year: 2020
Title: ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones.
Authors: Gyuhee Kim / Seong-Gyu Lee / Seungsu Han / Jaeeun Jung / Hyeong Seop Jeong / Jae-Kyung Hyun / Dong-Kwon Rhee / Ho Min Kim / Sangho Lee /
Abstract: AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly ...AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly modulated by their hexameric/dodecameric quaternary structures. Here we report the structural and biochemical characterizations of a tetradecameric AAA+ chaperone, ClpL from Streptococcus pneumoniae. ClpL exists as a tetradecamer in solution in the presence of ATP. The cryo-EM structure of ClpL at 4.5 Å resolution reveals a striking tetradecameric arrangement. Solution structures of ClpL derived from small-angle X-ray scattering data suggest that the tetradecameric ClpL could assume a spiral conformation found in active hexameric/dodecameric AAA+ chaperone structures. Vertical positioning of the middle domain accounts for the head-to-head arrangement of two heptameric rings. Biochemical activity assays with site-directed mutagenesis confirmed the critical roles of residues both in the integrity of the tetradecameric arrangement and activities of ClpL. Non-conserved Q321 and R670 are crucial in the heptameric ring assembly of ClpL. These results establish that ClpL is a functionally active tetradecamer, clearly distinct from hexameric/dodecameric AAA+ chaperones.
History
DepositionJan 21, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
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  • Surface view with fitted model
  • Atomic models: PDB-6lt4
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0967.png

Downloads & links

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Map

FileDownload / File: emd_0967.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 200 pix.
= 280. Å		1.4 Å/pix.
x 200 pix.
= 280. Å		1.4 Å/pix.
x 200 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.43583888 - 0.71694404
Average (Standard dev.)0.008872277 (±0.045397796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin282828
Dimensions200200200
Spacing200200200
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS282828
NC/NR/NS200200200
D min/max/mean-0.4360.7170.009

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Supplemental data

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Sample components

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Entire : AAA+ ATPase, chaperone

EntireName: AAA+ ATPase, chaperone
Components
  • Organelle or cellular component: AAA+ ATPase, chaperone
    • Protein or peptide: ATP-dependent Clp protease, ATP-binding subunit
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: AAA+ ATPase, chaperone

SupramoleculeName: AAA+ ATPase, chaperone / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: ATP-dependent Clp protease, ATP-binding subunit

MacromoleculeName: ATP-dependent Clp protease, ATP-binding subunit / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Molecular weightTheoretical: 77.599094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNNFNNFNN MDDLFNQLMG GMRGYSSENR RYLINGREVT PEEFAYYRAT GQLPGNAESD VQMQQQASGM KQDGVLAKLG RNLTAEARE GKLDPVIGRN KEIQEASEIL SRRTKNNPVL VGDAGVGKTA VVEGLAQAIV NGDVPAAIKN KEIVSIDISG L EAGTQYRG ...String:
MNNNFNNFNN MDDLFNQLMG GMRGYSSENR RYLINGREVT PEEFAYYRAT GQLPGNAESD VQMQQQASGM KQDGVLAKLG RNLTAEARE GKLDPVIGRN KEIQEASEIL SRRTKNNPVL VGDAGVGKTA VVEGLAQAIV NGDVPAAIKN KEIVSIDISG L EAGTQYRG SFEENVQNLV NEVKEAGNII LFFDAIHQIL GAGSTGGDSG SKGLADILKP ALSRGELTVI GATTQDEYRN TI LKNAALA RRFNEVKVNA PSAENTFKIL QGIRDLYQQH HNVILPDEVL KAAVDYSVQY IPQRSLPDKA IDLVDVTAAH LAA QHPVTD VHAVEREIET EKDKQEKAVE AEDFEAALNY KTRIAELERK IENHTEDMKV TASVNDVAES VERMTGIPVS QMGA SDIER LKDMAHRLQD KVIGQDKAVE VVARAICRNR AGFDEGNRPI GNFLFVGSTG VGKTELAKQL ALDMFGTQDA IIRLD MSEY SDRTAVSKLI GTTAGYVGYD DNSNTLTERV RRNPYSIILL DAIEKADPQV ITLLLQVLDD GRLTDGQGNT VNFKNT VII ATSNAGFGYE ANLTEDADKP ELMDRLKPFF RPEFLNRFNA VIEFSHLTKE DLSKIVDLML AEVNQTLAKK DIDLVVS QA AKDYITEEGY DEVMGVRPLR RVVEQEIRDK VTDFHLDHLD AKHLEADMED GVLVIREKV

UniProtKB: ATP-dependent Clp protease, ATP-binding subunit

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 28 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49797
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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