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- PDB-9cpk: D8 symmetry reconstruction of MmCPn in closed state -

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Basic information

Entry
Database: PDB / ID: 9cpk
TitleD8 symmetry reconstruction of MmCPn in closed state
ComponentsChaperonin
KeywordsCHAPERONE / Archaea chaperonin in closed state with ATP/AlFx
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily ...Thermosome, archaeal / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / : / Thermosome subunit
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 2.56 Å
AuthorsYanyan, Z.
Funding support3items
OrganizationGrant numberCountry
Other privateSilicon Valley Community Foundation CZI Imaging Initiative (2021-234593)
Other governmentU24GM139166
Other governmentU24GM129541
CitationJournal: To Be Published
Title: Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution
Authors: Yanyan, Z.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Chaperonin
J: Chaperonin
K: Chaperonin
L: Chaperonin
M: Chaperonin
A: Chaperonin
C: Chaperonin
D: Chaperonin
N: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
O: Chaperonin
P: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)941,83780
Polymers932,64416
Non-polymers9,19364
Water28816
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 , 1 types, 16 molecules BJKLMACDNEFGHIOP

#1: Protein
Chaperonin


Mass: 58290.262 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q877G8

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Non-polymers , 5 types, 80 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: subtomogram averaging

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Sample preparation

ComponentName: Archaea chaperonin MmCpn under ATP/AlFx condition / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Methanococcus maripaludis (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 39 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONvolume selection
2PHENIX1.21_5207:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160000 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 500 / Num. of volumes extracted: 160000

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