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- PDB-9wie: AMP-PNP bound E.coli CnoX-GroEL/ES complex, state IV -

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Basic information

Entry
Database: PDB / ID: 9wie
TitleAMP-PNP bound E.coli CnoX-GroEL/ES complex, state IV
Components
  • Chaperedoxin
  • Chaperonin GroEL
  • Co-chaperonin GroES
KeywordsCHAPERONE / Complex
Function / homology
Function and homology information


: / GroEL-GroES complex / chaperonin ATPase / virion assembly / isomerase activity / cell redox homeostasis / protein folding chaperone / ATP-dependent protein folding chaperone / response to radiation / protein refolding ...: / GroEL-GroES complex / chaperonin ATPase / virion assembly / isomerase activity / cell redox homeostasis / protein folding chaperone / ATP-dependent protein folding chaperone / response to radiation / protein refolding / : / response to heat / protein-folding chaperone binding / cellular response to oxidative stress / protein folding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Tetratricopeptide repeat / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Tetratricopeptide repeat / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. ...Tetratricopeptide repeat / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / 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 / GroES-like superfamily / Thioredoxin domain profile. / Thioredoxin domain / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Chaperonin GroEL / Co-chaperonin GroES / Chaperedoxin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsKim, J. / Roh, S.H.
Funding support Korea, Republic Of, 1items
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, S.H.
History
DepositionAug 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperonin GroEL
B: Chaperonin GroEL
C: Chaperonin GroEL
D: Chaperonin GroEL
E: Chaperonin GroEL
F: Chaperonin GroEL
G: Chaperonin GroEL
H: Co-chaperonin GroES
I: Co-chaperonin GroES
J: Co-chaperonin GroES
K: Co-chaperonin GroES
L: Co-chaperonin GroES
M: Co-chaperonin GroES
N: Co-chaperonin GroES
P: Chaperonin GroEL
R: Chaperonin GroEL
S: Chaperonin GroEL
T: Chaperonin GroEL
U: Chaperonin GroEL
V: Chaperonin GroEL
W: Chaperonin GroEL
d: Chaperedoxin
e: Chaperedoxin
f: Chaperedoxin
g: Chaperedoxin
h: Chaperedoxin
i: Chaperedoxin
j: Chaperedoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,106,68863
Polymers1,098,98828
Non-polymers7,70135
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 28 molecules ABCDEFGPRSTUVWHIJKLMNdefghij

#1: Protein
Chaperonin GroEL / 60 kDa chaperonin / Chaperonin-60 / Cpn60 / GroEL protein


Mass: 57391.711 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: groEL, groL, mopA, b4143, JW4103 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5, chaperonin ATPase
#2: Protein
Co-chaperonin GroES / 10 kDa chaperonin / Chaperonin-10 / Cpn10


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: groES, groS, mopB, b4142, JW4102 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F9
#3: Protein
Chaperedoxin / Heat shock protein CnoX / Trxsc


Mass: 31813.891 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cnoX, ybbN, b0492, JW5067 / Production host: Escherichia coli (E. coli) / References: UniProt: P77395

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Non-polymers , 3 types, 35 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AMP-PNP bound CnoX-GroEL/ES complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133737 / Symmetry type: POINT

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