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- EMDB-10529: Structure of the chaperonin gp146 from the bacteriophage EL (Pseu... -

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Basic information

Entry
Database: EMDB / ID: EMD-10529
TitleStructure of the chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ADP
Map dataStructure of gp146-ADP complex
Sample
  • Complex: The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ADP
    • Protein or peptide: Putative GroEL-like chaperonine protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsmolecular chaperone / ATPase / chaperonin / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Chaperone tailless complex polypeptide 1 (TCP-1) / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Putative GroEL-like chaperonine protein
Similarity search - Component
Biological speciesPseudomonas phage EL (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.91 Å
AuthorsBracher A / Wang H
CitationJournal: PLoS One / Year: 2020
Title: Structure and conformational cycle of a bacteriophage-encoded chaperonin.
Authors: Andreas Bracher / Simanta S Paul / Huping Wang / Nadine Wischnewski / F Ulrich Hartl / Manajit Hayer-Hartl /
Abstract: Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key ...Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism.
History
DepositionDec 5, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseApr 22, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tmw
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10529.png

Downloads & links

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Map

FileDownload / File: emd_10529.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of gp146-ADP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 160 pix.
= 319.52 Å		2 Å/pix.
x 160 pix.
= 319.52 Å		2 Å/pix.
x 160 pix.
= 319.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.997 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.10563626 - 0.34783676
Average (Standard dev.)0.0014802547 (±0.021807453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 319.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9971.9971.997
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z319.520319.520319.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1060.3480.001

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Supplemental data

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Sample components

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Entire : The chaperonin gp146 from the bacteriophage EL (Pseudomonas aerug...

EntireName: The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ADP
Components
  • Complex: The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ADP
    • Protein or peptide: Putative GroEL-like chaperonine protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: The chaperonin gp146 from the bacteriophage EL (Pseudomonas aerug...

SupramoleculeName: The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ADP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas phage EL (virus)
Molecular weightTheoretical: 864 KDa

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Macromolecule #1: Putative GroEL-like chaperonine protein

MacromoleculeName: Putative GroEL-like chaperonine protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage EL (virus)
Molecular weightTheoretical: 61.760941 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSQTLLVHGK DAQGIIKQVL SEVYDAVTST MGPNGQLVMI KNGVSTKTTK DGVTVARSIR FADEAHELVN RVITEPATKT DEECGDGTT TTIMLTHALY HLFKDFPGFQ HHRNIEDLVE RVIQRLESMA IRVEVDDPRL YQVALTSSNQ DEKLARLVSE L YANNKGSY ...String:
MSQTLLVHGK DAQGIIKQVL SEVYDAVTST MGPNGQLVMI KNGVSTKTTK DGVTVARSIR FADEAHELVN RVITEPATKT DEECGDGTT TTIMLTHALY HLFKDFPGFQ HHRNIEDLVE RVIQRLESMA IRVEVDDPRL YQVALTSSNQ DEKLARLVSE L YANNKGSY PDIELKEGVN FEDQIEQTTG RTIRMFYANP WFAKGHQGGV TELTGFTAFV IDRRIDKEDT QKLIDGVNHL VK THKQHLA LPILLIARSF EEAANSTLMQ LNAAHPTLVE DGRPWLIPLS TPVGGAIGTS ELQDIAVMLN APMLSDVADL TKL DTHSIN GQHGQLELGG NRSILKSTTP KDEDRIEQHA RGIEELLEGF SLSDKFSVRA RYNERRIRTL RGKLITISVG GETY SEVKE RVDRYEDVVK AIRSALENGI LPGGGVSLVK AVFGTIKEGL EDKDQSAEFA KRYINSGIAN ELMRLSTIQH KLLFK DTAL YKENGSFHFN DDWLNTPTVM NLATGEIGTP EGLGIYDTAY ASITALKGGL QTAKILATTK TLILGEKLSA VKVR

UniProtKB: Putative GroEL-like chaperonine protein

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 14 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*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

Concentration1.125 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
50.0 mMNaClsodium chloride
0.5 mMC10H16N2O8EDTA
4.0 mMMgCl2magnesium chloride
2.0 mMC10H15N5O10P2ADP
0.04 %C14H28O6beta-octyl glucoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time was 2 sec..

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 892 / Average exposure time: 0.074769 sec. / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 429456
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 5.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 170957
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 102119 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsJelly body refinement D7 symmetry NCS restraints
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6tmw:
Structure of the chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ADP

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