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- EMDB-24326: Methanococcus maripaludis chaperonin, open conformation 2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-24326
TitleMethanococcus maripaludis chaperonin, open conformation 2
Map data
Sample
  • Complex: MmCpn
    • Protein or peptide: Chaperonin
KeywordsOpen conformation / CHAPERONE
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
Biological speciesMethanococcus maripaludis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 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/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 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
DepositionJun 29, 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-7r9i
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24326.png

Downloads & links

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Map

FileDownload / File: emd_24326.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 AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.015165014 - 0.05268646
Average (Standard dev.)0.000060356902 (±0.0011490976)
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-0.0150.0530.000

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Supplemental data

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Sample components

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Entire : MmCpn

EntireName: MmCpn
Components
  • Complex: MmCpn
    • Protein or peptide: Chaperonin

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Supramolecule #1: MmCpn

SupramoleculeName: MmCpn / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (archaea)
Molecular weightTheoretical: 54.372539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RDAQRMNILA GRIIAETVRS TLGPKGMDKM LVDDLGDVVV TNDGVTILRE MSVEHPAAKM LIEVAKTQEK EVGDGTTTAV VVAGELLRK AEELLDQNVH PTIVVKGYQA AAQKAQELLK TIACEVGAQD KEILTKIAMT SITGKGAEKA KEKLAEIIVE A VSAVVDDE ...String:
RDAQRMNILA GRIIAETVRS TLGPKGMDKM LVDDLGDVVV TNDGVTILRE MSVEHPAAKM LIEVAKTQEK EVGDGTTTAV VVAGELLRK AEELLDQNVH PTIVVKGYQA AAQKAQELLK TIACEVGAQD KEILTKIAMT SITGKGAEKA KEKLAEIIVE A VSAVVDDE GKVDKDLIKI EKKSGASIDD TELIKGVLVD KERVSAQMPK KVTDAKIALL NCAIEIKETE TDAEIRITDP AK LMEFIEQ EEKMLKDMVA EIKASGANVL FCQKGIDDLA QHYLAKEGIV AARRVKKSDM EKLAKATGAN VITNIKDLSA QDL GDAGLV EERKISGDSM IFVEECKHPK AVTMLIRGTT EHVIEEVARA VDDAVGVVGC TIEDGRIVSG GGSTEVELSM KLRE YAEGI SGREQLAVRA FADALEVIPR TLAENAGLDA IEILVKVRAA HASNGNKCAG LNVFTGAVED MCENGVVEPL RVKTQ AIQS AAESTEMLLR IDDVIAAEKL R

UniProtKB: Thermosome subunit

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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: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3200
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7r9i:
Methanococcus maripaludis chaperonin, open conformation 2

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