[English] 日本語
Yorodumi
- EMDB-2326: Visualizing GroEL/ES in the Act of Encapsulating a Non-Native Sub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2326
TitleVisualizing GroEL/ES in the Act of Encapsulating a Non-Native Substrate Protein
Map dataSymmetry-free 3D reconstruction of the bullet-shaped substrate-encapsulated subpopulation sorted from the heterogeneous sample of EL43Py reacted with the substrate protein RuBisCO, GroES and nucleotide ATP
Sample
  • Sample: Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP
  • Protein or peptide: GroELcys0-D398A-S43C-pyrene
  • Protein or peptide: GroES
  • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase oxygenase
  • Ligand: Adenosine triphosphate
Keywordsprotein folding / chaperonin / GroEL / GroEL-GroES / cryo-EM / heterogeneity / substrate / RuBisCO / encapsulation
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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
Similarity search - Domain/homology
Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Rhodospirillum rubrum (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsChen D-H / Madan D / Weaver J / Lin Z / Schroder GF / Chiu W / Rye HS
CitationJournal: Cell / Year: 2013
Title: Visualizing GroEL/ES in the act of encapsulating a folding protein.
Authors: Dong-Hua Chen / Damian Madan / Jeremy Weaver / Zong Lin / Gunnar F Schröder / Wah Chiu / Hays S Rye /
Abstract: The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry- ...The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry-free, single-particle cryo-electron microscopy, we have characterized a chemically modified mutant of GroEL (EL43Py) that is trapped at a normally transient stage of substrate protein encapsulation. We show that the symmetric pattern of the GroEL subunits is broken as the GroEL cis-ring apical domains reorient to accommodate the simultaneous binding of GroES and an incompletely folded substrate protein (RuBisCO). The collapsed RuBisCO folding intermediate binds to the lower segment of two apical domains, as well as to the normally unstructured GroEL C-terminal tails. A comparative structural analysis suggests that the allosteric transitions leading to substrate protein release and folding involve concerted shifts of GroES and the GroEL apical domains and C-terminal tails.
History
DepositionMar 1, 2013-
Header (metadata) releaseMar 13, 2013-
Map releaseMar 13, 2013-
UpdateMar 26, 2014-
Current statusMar 26, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3zq0
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2326.png

Downloads & links

-
Map

FileDownload / File: emd_2326.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetry-free 3D reconstruction of the bullet-shaped substrate-encapsulated subpopulation sorted from the heterogeneous sample of EL43Py reacted with the substrate protein RuBisCO, GroES and nucleotide ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.04 Å/pix.
x 180 pix.
= 367.2 Å		2.04 Å/pix.
x 180 pix.
= 367.2 Å		2.04 Å/pix.
x 180 pix.
= 367.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-0.47194329 - 2.28602433
Average (Standard dev.)0.0433308 (±0.20919535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 367.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.042.042.04
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z367.200367.200367.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-12-40
NX/NY/NZ732581
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-0.4722.2860.043

-
Supplemental data

-
Sample components

-
Entire : Non-native RuBisCO substrate protein encapsulated inside the cavi...

EntireName: Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP
Components
  • Sample: Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP
  • Protein or peptide: GroELcys0-D398A-S43C-pyrene
  • Protein or peptide: GroES
  • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase oxygenase
  • Ligand: Adenosine triphosphate

-
Supramolecule #1000: Non-native RuBisCO substrate protein encapsulated inside the cavi...

SupramoleculeName: Non-native RuBisCO substrate protein encapsulated inside the cavity of GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP
type: sample / ID: 1000 / Details: This complex is bullet-shaped
Oligomeric state: Non-native RuBisCO substrate protein was encapsulated inside the cavity formed by one tetradecamer of GroEL variant EL43Py, one heptamer of GroES and seven nucleotides of ATP
Number unique components: 4
Molecular weightExperimental: 920 KDa / Theoretical: 920 KDa
Method: Estimated by the sum of GroEL molecular weight 800kDa, GroES molecular weight 70kDa and one RuBisCO monomer molecular weight 50kDa

-
Macromolecule #1: GroELcys0-D398A-S43C-pyrene

MacromoleculeName: GroELcys0-D398A-S43C-pyrene / type: protein_or_peptide / ID: 1 / Name.synonym: EL398A43Py
Details: A GroEL variant in which the endogenous Cys residues (138, 458, 519) have been changed to Ala (GroELcys0) was modified to contain two additional mutations: D398A and S43C. The D398A mutation ...Details: A GroEL variant in which the endogenous Cys residues (138, 458, 519) have been changed to Ala (GroELcys0) was modified to contain two additional mutations: D398A and S43C. The D398A mutation prevents ATP hydrolysis by GroEL, while the S43C mutation, located at the tip of stem loop at the bottom of the GroEL cavity, permits the covalent attachment of N-1-pyrene maleimide to this position.
Number of copies: 14 / Oligomeric state: Tetradecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Location in cell: Cytoplasm
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pACYC
SequenceUniProtKB: Chaperonin GroEL

-
Macromolecule #2: GroES

MacromoleculeName: GroES / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Oligomeric state: Heptamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightExperimental: 70 KDa / Theoretical: 70 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pACYC
SequenceUniProtKB: Co-chaperonin GroES

-
Macromolecule #3: Ribulose-1,5-bisphosphate carboxylase oxygenase

MacromoleculeName: Ribulose-1,5-bisphosphate carboxylase oxygenase / type: protein_or_peptide / ID: 3 / Name.synonym: RuBisCO
Details: The native RuBisCO is a dimer, but the encapsulated RuBisCO is a non-native monomer.
Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Rhodospirillum rubrum (bacteria) / Location in cell: cytoplasm
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pUC derived plasmid with T7 promoter

-
Macromolecule #4: Adenosine triphosphate

MacromoleculeName: Adenosine triphosphate / type: ligand / ID: 4 / Name.synonym: ATP / Number of copies: 7 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.4 mg/mL
BufferpH: 7.6 / Details: 50 mM Hepes, 50 mM KOAc, 10 mM Mg(OAc)2, 2 mM DTT
GridDetails: 400 mesh R1.2/1.3 Quantifoil grid glow-discharged 10 sec before freezing
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 98 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 1 second before plunging

-
Electron microscopy

MicroscopeJEOL 3000SFF
TemperatureMin: 50 K / Max: 51 K / Average: 50.5 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
DateAug 16, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 15 µm / Number real images: 2379 / Average electron dose: 30 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 73530 / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 1.6 mm / Nominal defocus max: 4.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Helium cooled top-entry cartridge / Specimen holder model: OTHER

+
Image processing

DetailsParticle selection was performed semi-automatically using the EMAN1 program, boxer. The contrast transfer function fitting was performed automatically using the program fitctf.py and then fine-tuned manually using the EMAN1 program ctfit. The methodology of EMAN1 multiple-model refinement (EMAN1 program multirefine) for compositionally and conformationally heterogeneous complex analysis was used to sort out the relatively homogeneous bullet-shaped particle images with the substrate protein inside the cis cavity.
CTF correctionDetails: Each frame
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: OTHER / Software - Name: EMAN1 / Number images used: 17611
Final angle assignmentDetails: EMAN1
Final two d classificationNumber classes: 711

-
Atomic model buiding 1

Initial modelPDB ID:

1aon


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U
SoftwareName: DireX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model

PDB-3zq0:
Visualizing GroEL-ES in the Act of Encapsulating a Non-Native Substrate Protein

+
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