[English] 日本語
Yorodumi
- EMDB-3051: Structure and mechanism of the Rubisco assembly chaperone Raf1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3051
TitleStructure and mechanism of the Rubisco assembly chaperone Raf1
Map dataNegative stain 3D reconstruction of Thermosynechococcus elongatus RbcL8 Raf14
Sample
  • Sample: Thermosynechococcus elongatus RbcL/Raf1
  • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase oxygenase
  • Protein or peptide: Rubisco accumulation factor 1
KeywordsRubisco / Chaperone / Raf1 / assembly
Function / homologyChaperonin-like RbcX
Function and homology information
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 24.8 Å
AuthorsHauser A / Bhat JY / Milicic G / Wendler P / Hartl FU / Bracher A / Hayer-Hartl M
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structure and mechanism of the Rubisco-assembly chaperone Raf1.
Authors: Thomas Hauser / Javaid Y Bhat / Goran Miličić / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation ...Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation factor1 (Raf1), a dimer of ∼40-kDa subunits. We find that Raf1 from Synechococcus elongatus acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by RbcS results in holoenzyme formation. Crystal structures show that Raf1 from Arabidopsis thaliana consists of a β-sheet dimerization domain and a flexibly linked α-helical domain. Chemical cross-linking and EM reconstruction indicate that the β-domains bind along the equator of each RbcL2 unit, and the α-helical domains embrace the top and bottom edges of RbcL2. Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.
History
DepositionJun 19, 2015-
Header (metadata) releaseJul 15, 2015-
Map releaseAug 5, 2015-
UpdateSep 23, 2015-
Current statusSep 23, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB3051.png

Downloads & links

-
Map

FileDownload / File: emd_3051.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain 3D reconstruction of Thermosynechococcus elongatus RbcL8 Raf14
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 192 pix.
= 414.72 Å		2.16 Å/pix.
x 192 pix.
= 414.72 Å		2.16 Å/pix.
x 192 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.005 / Movie #1: 0.026
Minimum - Maximum-0.07808658 - 0.05269519
Average (Standard dev.)-0.00362806 (±0.01118839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.162.162.16
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720414.720
α/β/γ90.00090.00090.000
start NX/NY/NZ-21-120
NX/NY/NZ432573
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0780.053-0.004

-
Supplemental data

-
Sample components

-
Entire : Thermosynechococcus elongatus RbcL/Raf1

EntireName: Thermosynechococcus elongatus RbcL/Raf1
Components
  • Sample: Thermosynechococcus elongatus RbcL/Raf1
  • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase oxygenase
  • Protein or peptide: Rubisco accumulation factor 1

-
Supramolecule #1000: Thermosynechococcus elongatus RbcL/Raf1

SupramoleculeName: Thermosynechococcus elongatus RbcL/Raf1 / type: sample / ID: 1000 / Oligomeric state: Four Raf1 dimers bind one RbcL octamer / Number unique components: 2
Molecular weightExperimental: 743 KDa / Theoretical: 741 KDa / Method: native Mass Spectrometry

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

MacromoleculeName: Ribulose-1,5-bisphosphate carboxylase oxygenase / type: protein_or_peptide / ID: 1 / Name.synonym: RuBisCO / Number of copies: 8 / Oligomeric state: Octamer / Recombinant expression: Yes
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Organelle: Chloroplast
Molecular weightTheoretical: 43 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pDuet
SequenceInterPro: Chaperonin-like RbcX

-
Macromolecule #2: Rubisco accumulation factor 1

MacromoleculeName: Rubisco accumulation factor 1 / type: protein_or_peptide / ID: 2 / Name.synonym: Raf1 / Number of copies: 8 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Organelle: Chloroplast
Molecular weightTheoretical: 40 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pDuet

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.5 / Details: 20mM MOPS-KOH, 100mM KCl, 5mM Mg acetate, 5mM DTT
StainingType: NEGATIVE / Details: Grids were stained with 2% uranyl acetate for 30s
GridDetails: Plasma cleaned carbon coated grids (Quantifoil)
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Detailslow dose
DateDec 17, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 90 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: negative stain / Specimen holder model: SIDE ENTRY, EUCENTRIC

-
Image processing

Detailsparticles were selected manually
CTF correctionDetails: Relion
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.8 Å / Resolution method: OTHER / Software - Name: MRC, Imagic, RELION, 1.3 / Number images used: 5471

+
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