[English] 日本語
Yorodumi
- PDB-2wvw: Cryo-EM structure of the RbcL-RbcX complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wvw
TitleCryo-EM structure of the RbcL-RbcX complex
Components
  • RBCX PROTEIN
  • RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
KeywordsPHOTOSYNTHESIS / COMPLEX ASSEMBLY / PHOTORESPIRATION / DISULFIDE BOND / CARBON FIXATION / LYASE / CHAPERONE / CALVIN CYCLE / CARBON DIOXIDE FIXATION / MONOOXYGENASE / METAL-BINDING / OXIDOREDUCTASE
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / carbon fixation / photosynthesis / protein folding chaperone / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / carbon fixation / photosynthesis / protein folding chaperone / monooxygenase activity / magnesium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / 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 chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / 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
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
ANABAENA SP. CA (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsLiu, C. / Young, A.L. / Starling-Windhof, A. / Bracher, A. / Saschenbrecker, S. / Rao, B.V. / Rao, K.V. / Berninghausen, O. / Mielke, T. / Hartl, F.U. ...Liu, C. / Young, A.L. / Starling-Windhof, A. / Bracher, A. / Saschenbrecker, S. / Rao, B.V. / Rao, K.V. / Berninghausen, O. / Mielke, T. / Hartl, F.U. / Beckmann, R. / Hayer-Hartl, M.
CitationJournal: Nature / Year: 2010
Title: Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich ...Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich Hartl / Roland Beckmann / Manajit Hayer-Hartl /
Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The ...Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.
History
DepositionOct 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Other / Version format compliance
Revision 1.2Jun 6, 2012Group: Other
Revision 1.3Aug 30, 2017Group: Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.4Oct 3, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / em_software
Item: _em_sample_support.grid_type / _em_software.image_processing_id
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.6Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1654
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1655
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1656
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
B: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
D: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
F: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
H: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RBCX PROTEIN
J: RBCX PROTEIN
K: RBCX PROTEIN
L: RBCX PROTEIN
M: RBCX PROTEIN
N: RBCX PROTEIN
O: RBCX PROTEIN
P: RBCX PROTEIN
Q: RBCX PROTEIN
R: RBCX PROTEIN
S: RBCX PROTEIN
T: RBCX PROTEIN
U: RBCX PROTEIN
V: RBCX PROTEIN
W: RBCX PROTEIN
X: RBCX PROTEIN


Theoretical massNumber of molelcules
Total (without water)703,25224
Polymers703,25224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

-
Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RBCL / RUBISCO LARGE SUBUNIT


Mass: 52516.605 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 6301 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P00880, ribulose-bisphosphate carboxylase
#2: Protein
RBCX PROTEIN / RUBISCO ASSEMBLY CHAPERONE


Mass: 17694.930 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. CA (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q44212
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RBCL8-X8 RUBISCO ASSEMBLY INTERMEDIATE CONTAINING 8 COPIES OF THE LARGE RUBISCO SUBUNIT RBCL AND EIGHT COPIES OF THE DIMERIC ASSEMBLY CHAPERONE RBCX2.
Type: COMPLEX
Buffer solutionName: 20 MM TRIS-HCL, PH 8.7 / pH: 8.7 / Details: 20 MM TRIS-HCL, PH 8.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL GRIDS (3/3) WITH 2 NM CARBON ON TOP / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: VITROBOT USED, LIQUID ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38900 X / Nominal defocus max: 3100 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm
Specimen holderTemperature: 85 K / Tilt angle max: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 56
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: EMAN / Version: 1 / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: STANDARD EMAN REFINE PROCEDURE / Resolution: 9 Å / Num. of particles: 11104 / Nominal pixel size: 1.63 Å / Actual pixel size: 1.63 Å / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Details: METHOD--MANUAL
Atomic model buildingPDB-ID: 3HYB

3hyb


Accession code: 3HYB / Source name: PDB / Type: experimental model
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42392 0 0 0 42392

+
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