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- EMDB-14352: Structure of the GroEL chaperonin in complex with the CnoX chaper... -

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Basic information

Entry
Database: EMDB / ID: EMD-14352
TitleStructure of the GroEL chaperonin in complex with the CnoX chaperedoxin
Map dataMap generated by phenix.resolve after relion refinement
Sample
  • Complex: 1:1 stoichiometric complex of GroEL-CnoX
    • Protein or peptide: Chaperedoxin
    • Protein or peptide: Chaperonin GroEL
KeywordsProtein Folding / Redox / Complex / Chaperonin / CHAPERONE
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsVan der Verren SE / Remaut H
Funding support Belgium, 2 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Fonds de la Recherche Scientifique (FNRS)WELBIO-CR-2019C-03 Belgium
CitationJournal: To Be Published
Title: A molecular plugin rescues GroEL/ES substrates from pre-folding oxidation
Authors: Dupuy E / Van der Verren SE / Lin J / Wilson M / Viela F / Latour E / Dachsbeck A / Gennaris A / Vertommen D / Dufresne Y / Iorga B / Goemans CV / Remaut H / Collet JF
History
DepositionFeb 15, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14352.png

Downloads & links

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Map

FileDownload / File: emd_14352.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap generated by phenix.resolve after relion refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 200 pix.
= 313.6 Å		1.57 Å/pix.
x 200 pix.
= 313.6 Å		1.57 Å/pix.
x 200 pix.
= 313.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.568 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-1.0553399 - 1.4577162
Average (Standard dev.)-0.0000071598015 (±0.051087316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 313.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local sharpened map as generated by LocScale to help visualise CnoX

Fileemd_14352_additional_1.map
AnnotationLocal sharpened map as generated by LocScale to help visualise CnoX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 1:1 stoichiometric complex of GroEL-CnoX

EntireName: 1:1 stoichiometric complex of GroEL-CnoX
Components
  • Complex: 1:1 stoichiometric complex of GroEL-CnoX
    • Protein or peptide: Chaperedoxin
    • Protein or peptide: Chaperonin GroEL

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Supramolecule #1: 1:1 stoichiometric complex of GroEL-CnoX

SupramoleculeName: 1:1 stoichiometric complex of GroEL-CnoX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Chaperedoxin

MacromoleculeName: Chaperedoxin / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.771923 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADTPEIQQLQ QQVAENPEDA ALATQLALQL HQVGRNEEAL ELLFGHLRKD LTAADGQTRK TFQEILAALG TGDALASKYR RQLYALLY

UniProtKB: UNIPROTKB: A0A7U2VUH6

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Macromolecule #2: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 55.220105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV ...String:
AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV GKEGVITVED GTGLQDELDV VEGMQFDRGY LSPYFINKPE TGAVELESPF ILLADKKISN IREMLPVLEA VA KAGKPLL IIAEDVEGEA LATLVVNTMR GIVKVAAVKA PGFGDRRKAM LQDIATLTGG TVISEEIGME LEKATLEDLG QAK RVVINK DTTTIIDGVG EEAAIQGRVA QIRQQIEEAT SDYDREKLQE RVAKLAGGVA VIKVGAATEV EMKEKKARVE DALH ATRAA VEEGVVAGGG VALIRVASKL ADLRGQNEDQ NVGIKVALRA MEAPLRQIVL NCGEEPSVVA NTVKGGDGNY GYNAA TEEY GNMIDMGILD PTKVTRSALQ YAASVAGLMI TTECMVTDLP

UniProtKB: UNIPROTKB: A0A828EVF1

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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

Concentration0.4 mg/mL
BufferpH: 8 / Details: 50mM Tris pH=8, 150mM NaCl, 1mM EDTA
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3
DetailsStrep-affinity purified complex

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000

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Image processing

Particle selectionNumber selected: 670080
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 170458
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1grl

source_name: PDB, initial_model_type: experimental model

3qou

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coeficient
Output model

PDB-7ywy:
Structure of the GroEL chaperonin in complex with the CnoX chaperedoxin

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