[English] 日本語
Yorodumi
- EMDB-24328: Methanococcus maripaludis chaperonin, closed conformation 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24328
TitleMethanococcus maripaludis chaperonin, closed conformation 4
Map data
Sample
  • Complex: MmCpn
    • Protein or peptide: Chaperonin
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP 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 / 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: 4.1 Å
AuthorsZhao Y / Schmid M / Frydman J / Chiu W
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-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7r9k
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24328.png

Downloads & links

-
Map

FileDownload / File: emd_24328.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.016901242 - 0.07969994
Average (Standard dev.)6.2063926e-05 (±0.0012405654)
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-0.0170.0800.000

-
Supplemental data

-
Sample components

-
Entire : MmCpn

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

-
Supramolecule #1: MmCpn

SupramoleculeName: MmCpn / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanococcus maripaludis (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1 MDa

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238000

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7r9k:
Methanococcus maripaludis chaperonin, closed conformation 4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more