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- EMDB-65877: AMP-PNP bound E.coli CnoX-GroEL complex, state I -

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Basic information

Entry
Database: EMDB / ID: EMD-65877
TitleAMP-PNP bound E.coli CnoX-GroEL complex, state I
Map dataCnoX-GroEL complex (State I)
Sample
  • Complex: AMP-PNP bound CnoX-GroEL complex
    • Protein or peptide: Chaperedoxin
    • Protein or peptide: Chaperonin GroEL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsComplex / CHAPERONE
Function / homology
Function and homology information


: / GroEL-GroES complex / chaperonin ATPase / virion assembly / isomerase activity / cell redox homeostasis / ATP-dependent protein folding chaperone / response to radiation / protein refolding / : ...: / GroEL-GroES complex / chaperonin ATPase / virion assembly / isomerase activity / cell redox homeostasis / ATP-dependent protein folding chaperone / response to radiation / protein refolding / : / response to heat / cellular response to oxidative stress / protein folding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / Thioredoxin / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family ...Tetratricopeptide repeat / Tetratricopeptide repeat / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / Thioredoxin / 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 / Thioredoxin domain profile. / Thioredoxin domain / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Chaperonin GroEL / Chaperedoxin
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsKim J / Roh SH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structural interplay of the redox co-chaperone CnoX to GroEL/ES chaperonin
Authors: Kim J / Jung M / Roh SH
History
DepositionAug 18, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65877.png

Downloads & links

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Map

FileDownload / File: emd_65877.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCnoX-GroEL complex (State I)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.011964513 - 2.0187244
Average (Standard dev.)0.0073767914 (±0.06555447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map before pre-processing

Fileemd_65877_additional_1.map
AnnotationMap before pre-processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65877_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65877_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AMP-PNP bound CnoX-GroEL complex

EntireName: AMP-PNP bound CnoX-GroEL complex
Components
  • Complex: AMP-PNP bound CnoX-GroEL complex
    • Protein or peptide: Chaperedoxin
    • Protein or peptide: Chaperonin GroEL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: AMP-PNP bound CnoX-GroEL complex

SupramoleculeName: AMP-PNP bound CnoX-GroEL complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K12 (bacteria)

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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 K-12 (bacteria)
Molecular weightTheoretical: 31.813891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVENIVNIN ESNLQQVLEQ SMTTPVLFYF WSERSQHCLQ LTPILESLAA QYNGQFILAK LDCDAEQMIA AQFGLRAIPT VYLFQNGQP VDGFQGPQPE EAIRALLDKV LPREEELKAQ QAMQLMQESN YTDALPLLKD AWQLSNQNGE IGLLLAETLI A LNRSEDAE ...String:
MSVENIVNIN ESNLQQVLEQ SMTTPVLFYF WSERSQHCLQ LTPILESLAA QYNGQFILAK LDCDAEQMIA AQFGLRAIPT VYLFQNGQP VDGFQGPQPE EAIRALLDKV LPREEELKAQ QAMQLMQESN YTDALPLLKD AWQLSNQNGE IGLLLAETLI A LNRSEDAE AVLKTIPLQD QDTRYQGLVA QIELLKQAAD TPEIQQLQQQ VAENPEDAAL ATQLALQLHQ VGRNEEALEL LF GHLRKDL TAADGQTRKT FQEILAALGT GDALASKYRR QLYALLY

UniProtKB: Chaperedoxin

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Macromolecule #2: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 57.391711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG IDKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG K LIAEAMDK ...String:
MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG IDKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG K LIAEAMDK VGKEGVITVE DGTGLQDELD VVEGMQFDRG YLSPYFINKP ETGAVELESP FILLADKKIS NIREMLPVLE AV AKAGKPL LIIAEDVEGE ALATLVVNTM RGIVKVAAVK APGFGDRRKA MLQDIATLTG GTVISEEIGM ELEKATLEDL GQA KRVVIN KDTTTIIDGV GEEAAIQGRV AQIRQQIEEA TSDYDREKLQ ERVAKLAGGV AVIKVGAATE VEMKEKKARV EDAL HATRA AVEEGVVAGG GVALIRVASK LADLRGQNED QNVGIKVALR AMEAPLRQIV LNCGEEPSVV ANTVKGGDGN YGYNA ATEE YGNMIDMGIL DPTKVTRSAL QYAASVAGLM ITTECMVTDL PKNDAADLGA AGGMGGMGGM GGMM

UniProtKB: Chaperonin GroEL

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 14 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 14 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 214141
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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