[English] 日本語
Yorodumi
- EMDB-3699: Structure of Rubisco from Rhodobacter sphaeroides in complex with CABP -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3699
TitleStructure of Rubisco from Rhodobacter sphaeroides in complex with CABP
Map datapostprocessed Rubisco map; D4 symmetry
SampleRubisco
  • (Ribulose bisphosphate carboxylase ...RuBisCO) x 2
  • (ligand) x 2
Function / homologyRuBisCO / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / Ribulose bisphosphate carboxylase small chain, domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large subunit, type I ...RuBisCO / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / Ribulose bisphosphate carboxylase small chain, domain / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase large chain, catalytic domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / Ribulose bisphosphate carboxylase, small subunit superfamily / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small chain 1
Function and homology information
SourceRhodobacter sphaeroides (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.39 Å resolution
AuthorsBracher A / Milicic G
CitationJournal: Mol. Cell / Year: 2017
Title: Mechanism of Enzyme Repair by the AAA Chaperone Rubisco Activase.
Authors: Javaid Y Bhat / Goran Miličić / Gabriel Thieulin-Pardo / Andreas Bracher / Andrew Maxwell / Susanne Ciniawsky / Oliver Mueller-Cajar / John R Engen / F Ulrich Hartl / Petra Wendler / Manajit Hayer-Hartl
Abstract: How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) ...How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.
Validation ReportPDB-ID: 5nv3

SummaryFull reportAbout validation report
DateDeposition: May 3, 2017 / Header (metadata) release: May 10, 2017 / Map release: Jul 26, 2017 / Last update: Sep 20, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5nv3
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3699.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.04 Å/pix.
= 332.8 Å
320 pix
1.04 Å/pix.
= 332.8 Å
320 pix
1.04 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.9 (by author), 0.9 (movie #1):
Minimum - Maximum-8.962299 - 10.2346325
Average (Standard dev.)0.0022220209 (0.27295503)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-8.96210.2350.002

-
Supplemental data

-
Sample components

+
Entire Rubisco

EntireName: Rubisco / Details: Rubisco was treated with the inhibitor CABP. / Number of components: 5

+
Component #1: protein, Rubisco

ProteinName: Rubisco / Details: Rubisco was treated with the inhibitor CABP. / Recombinant expression: No
SourceSpecies: Rhodobacter sphaeroides (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #2: protein, Ribulose bisphosphate carboxylase large chain

ProteinName: Ribulose bisphosphate carboxylase large chain / Recombinant expression: No
MassTheoretical: 51.768852 kDa
Source (engineered)Expression System: Rhodobacter sphaeroides (bacteria)

+
Component #3: protein, Ribulose bisphosphate carboxylase small chain 1

ProteinName: Ribulose bisphosphate carboxylase small chain 1 / Recombinant expression: No
MassTheoretical: 15.183234 kDa
Source (engineered)Expression System: Rhodobacter sphaeroides (bacteria)

+
Component #4: ligand, 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

LigandName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.356115 kDa

+
Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Cs corrected Krios 1 at NeCEN (June 2016)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D4 (2*4 fold dihedral) / Number of projections: 333122
3D reconstructionSoftware: RELION / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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