[English] 日本語
Yorodumi
- PDB-8baa: CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8baa
TitleCryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II.
Components
  • Chaperonin GroEL
  • Co-chaperonin GroES
  • Ribulose bisphosphate carboxylase
KeywordsCHAPERONE / GroEL / GroES
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / GroEL-GroES complex / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chaperonin ATPase / virion assembly / : / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone ...ribulose-bisphosphate carboxylase / GroEL-GroES complex / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chaperonin ATPase / virion assembly / : / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / monooxygenase activity / 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 / metal ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal ...Ribulose bisphosphate carboxylase large subunit, type II / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / 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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / : / Chaperonin GroEL / Co-chaperonin GroES / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Rhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGardner, S. / Saibil, H.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009513/1 United Kingdom
CitationJournal: To Be Published
Title: CryoEM snapshots of non-native Rubisco bound to GroEL, GroEL-ADP.BeF3, and GroEL-GroES.
Authors: Gardner, S. / Lukyanova, N. / Darrow, M.C. / Thalassinos, K. / Saibil, H.R.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperonin GroEL
B: Chaperonin GroEL
C: Chaperonin GroEL
D: Chaperonin GroEL
E: Chaperonin GroEL
F: Chaperonin GroEL
G: Chaperonin GroEL
H: Chaperonin GroEL
I: Chaperonin GroEL
J: Chaperonin GroEL
K: Chaperonin GroEL
L: Chaperonin GroEL
M: Chaperonin GroEL
N: Chaperonin GroEL
O: Co-chaperonin GroES
P: Co-chaperonin GroES
Q: Co-chaperonin GroES
R: Co-chaperonin GroES
S: Co-chaperonin GroES
T: Co-chaperonin GroES
U: Co-chaperonin GroES
Z: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)932,17564
Polymers924,99322
Non-polymers7,18342
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area77200 Å2
ΔGint-613 kcal/mol
Surface area349260 Å2

-
Components

-
Protein , 3 types, 22 molecules ABCDEFGHIJKLMNOPQRSTUZ

#1: Protein
Chaperonin GroEL / 60 kDa chaperonin / Chaperonin-60 / Cpn60 / GroEL protein


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: groEL, groL, mopA, b4143, JW4103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6F5, chaperonin ATPase
#2: Protein
Co-chaperonin GroES / 10 kDa chaperonin / Chaperonin-10 / Cpn10


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: groES, groS, mopB, b4142, JW4102 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6F9
#3: Protein Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50538.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1
Gene: cbbM, Rru_A2400 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2RRP5, ribulose-bisphosphate carboxylase

-
Non-polymers , 4 types, 42 molecules

#4: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: GroEL-GroES-ADP.AlF3-Rubisco / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.802 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTrcESL
Buffer solutionpH: 7.5
SpecimenConc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 293 K
Details: The grid was prepared using a chameleon (SPT Labtech).

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 40.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
10RELION3.1initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7712622
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8237 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 216.04 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003663429
ELECTRON MICROSCOPYf_angle_d0.836585709
ELECTRON MICROSCOPYf_chiral_restr0.074610334
ELECTRON MICROSCOPYf_plane_restr0.009311161
ELECTRON MICROSCOPYf_dihedral_angle_d10.6059104

+
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