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- EMDB-24363: Methanococcus maripaludis chaperonin complex in open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-24363
TitleMethanococcus maripaludis chaperonin complex in open conformation
Map data
Sample
  • Complex: Ternary complex of chaperonin MmCpn in open state under ATP condition
    • Protein or peptide: Chaperonin
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsComplex / chaperonin. / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / protein-containing complex / ATP binding / metal ion binding / identical protein binding / cytoplasm
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
Biological speciesMethanococcus maripaludis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhao Y / Schmid M
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)P01NS092525 United States
National Institutes of Health/Office of the DirectorS10OD021600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM07407411 United States
National Institutes of Health/Office of the DirectorP41GM103832 United States
CitationJournal: Nat Commun / Year: 2021
Title: CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin.
Authors: Yanyan Zhao / Michael F Schmid / Judith Frydman / Wah Chiu /
Abstract: Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism ...Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.
History
DepositionJul 1, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rak
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24363.png

Downloads & links

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Map

FileDownload / File: emd_24363.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 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 EMDB: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.14280738 - 0.23673907
Average (Standard dev.)0.0008621986 (±0.009149571)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
start NX/NY/NZ594743
NX/NY/NZ375263
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1430.2370.001

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Supplemental data

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Sample components

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Entire : Ternary complex of chaperonin MmCpn in open state under ATP condition

EntireName: Ternary complex of chaperonin MmCpn in open state under ATP condition
Components
  • Complex: Ternary complex of chaperonin MmCpn in open state under ATP condition
    • Protein or peptide: Chaperonin
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Ternary complex of chaperonin MmCpn in open state under ATP condition

SupramoleculeName: Ternary complex of chaperonin MmCpn in open state under ATP condition
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Chaperonin

MacromoleculeName: Chaperonin / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 54.560789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGRDAQRMNI LAGRIIAETV RSTLGPKGMD KMLVDDLGDV VVTNDGVTIL REMSVEHPAA KMLIEVAKTQ EKEVGDGTTT AVVVAGELL RKAEELLDQN VHPTIVVKGY QAAAQKAQEL LKTIACEVGA QDKEILTKIA MTSITGKGAE KAKEKLAEII V EAVSAVVD ...String:
MGRDAQRMNI LAGRIIAETV RSTLGPKGMD KMLVDDLGDV VVTNDGVTIL REMSVEHPAA KMLIEVAKTQ EKEVGDGTTT AVVVAGELL RKAEELLDQN VHPTIVVKGY QAAAQKAQEL LKTIACEVGA QDKEILTKIA MTSITGKGAE KAKEKLAEII V EAVSAVVD DEGKVDKDLI KIEKKSGASI DDTELIKGVL VDKERVSAQM PKKVTDAKIA LLNCAIEIKE TETDAEIRIT DP AKLMEFI EQEEKMLKDM VAEIKASGAN VLFCQKGIDD LAQHYLAKEG IVAARRVKKS DMEKLAKATG ANVITNIKDL SAQ DLGDAG LVEERKISGD SMIFVEECKH PKAVTMLIRG TTEHVIEEVA RAVDDAVGVV GCTIEDGRIV SGGGSTEVEL SMKL REYAE GISGREQLAV RAFADALEVI PRTLAENAGL DAIEILVKVR AAHASNGNKC AGLNVFTGAV EDMCENGVVE PLRVK TQAI QSAAESTEML LRIDDVIAAE KLR

UniProtKB: Thermosome subunit

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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