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- EMDB-0204: OBP chaperonin in the nucleotide-free state -

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Basic information

Entry
Database: EMDB / ID: EMD-0204
TitleOBP chaperonin in the nucleotide-free state
Map dataA symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the nucleotide-free state.
Sample
  • Complex: OBP chaperonin in the nucleotide-free state
    • Protein or peptide: Putative chaperonin GroEL
Keywordschaperonin / nucleotide-free / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP 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 chaperonin GroEL
Similarity search - Component
Biological speciesPseudomonas phage OBP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsStanishneva-Konovalova TB / Pichkur EB / Sokolova OS
Funding support Russian Federation, 2 items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-04-00605 Russian Federation
Russian Foundation for Basic Research18-04-01281 Russian Federation
CitationJournal: J Struct Biol / Year: 2020
Title: Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin.
Authors: Tatiana B Stanishneva-Konovalova / Pavel I Semenyuk / Lidia P Kurochkina / Evgeny B Pichkur / Alexander L Vasilyev / Mikhail V Kovalchuk / Mikhail P Kirpichnikov / Olga S Sokolova /
Abstract: Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They ...Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.
History
DepositionAug 17, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseAug 28, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.09
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  • Surface view with fitted model
  • Atomic models: PDB-6hdd
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0204.png

Downloads & links

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Map

FileDownload / File: emd_0204.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the nucleotide-free state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.06988939 - 0.22754554
Average (Standard dev.)0.0021357222 (±0.02195315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0700.2280.002

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Supplemental data

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Additional map: A symmetry-free cryo-EM structure of a single-ring chaperonin...

Fileemd_0204_additional.map
AnnotationA symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the nucleotide-free state.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OBP chaperonin in the nucleotide-free state

EntireName: OBP chaperonin in the nucleotide-free state
Components
  • Complex: OBP chaperonin in the nucleotide-free state
    • Protein or peptide: Putative chaperonin GroEL

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Supramolecule #1: OBP chaperonin in the nucleotide-free state

SupramoleculeName: OBP chaperonin in the nucleotide-free state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage OBP (virus)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Putative chaperonin GroEL

MacromoleculeName: Putative chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage OBP (virus)
Molecular weightTheoretical: 57.259703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TEISFTNKND TREIVDEVVE NAFSSVCSTM GPNGNYVVIN QLNSPKVTKD GVSVARALDF NEARRNMIAK IITEPSIKTD AEVGDGTTT TVFITYHLYQ KFKDAMSFAN TRYLDTLIKQ VLQYIGTLIQ PGEIESEMFR NMLLTSSNYE EEIVDKILDI Y REHKNPNI ...String:
TEISFTNKND TREIVDEVVE NAFSSVCSTM GPNGNYVVIN QLNSPKVTKD GVSVARALDF NEARRNMIAK IITEPSIKTD AEVGDGTTT TVFITYHLYQ KFKDAMSFAN TRYLDTLIKQ VLQYIGTLIQ PGEIESEMFR NMLLTSSNYE EEIVDKILDI Y REHKNPNI HLEKSPMLPA DEVKMTKEIY FEGSFPIETQ VPANGAYVVG PEKVGVVLID GSIRAYPTQL INALLNRFID NP VVLMARN FEPEVIAAIN NENQRLGTSR IFAYKVNAAG LLGAGTIDDL GRLLNIGPVF DVNSVDPALV KYNDVTLWLG RKG ILLDKS IEEVESRADS ILEGLDNRYE ALGIIERQTP IGRELNRRIG RLRANNVTIK VTGVTVSDAS ERWARYEDVM KAAR TGQQF GVIPGIGYGY LMASKWLEAN VPQQSDEKLE KCRIGLIEVL RAQYEHLTGH DGSAENPIFI DLVTGQESDT PMNVY DNAA ATMIALEGAW QTAKTLGKIS NVMGRSNTNY A

UniProtKB: Putative chaperonin GroEL

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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

Concentration2.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127180
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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