[English] 日本語
Yorodumi
- EMDB-22308: EPYC1(49-72)-bound Rubisco -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22308
TitleEPYC1(49-72)-bound Rubisco
Map dataEPYC1(49-72) peptide-bound Rubisco. The map was processed at super resolution pixel size
Sample
  • Complex: EPYC1(49-72) peptide-bound Rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
    • Protein or peptide: LCI5
  • Ligand: water
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast stroma / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / 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, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / 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 / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 / LCI5
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.13 Å
AuthorsChou H / Matthies D / He S / Jonikas MC / Yu Z
Funding support United States, Singapore, United Kingdom, 9 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1359682 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM-119137 United States
National Science Foundation (NSF, United States)MCB-1935444 United States
Ministry of Education (MoE, Singapore)MOE2018-T2-2-059 Singapore
Howard Hughes Medical Institute (HHMI)55108535 United States
Leverhulme TrustRPG-2017-402 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S015531/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007276 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
CitationJournal: Nat Plants / Year: 2020
Title: The structural basis of Rubisco phase separation in the pyrenoid.
Authors: Shan He / Hui-Ting Chou / Doreen Matthies / Tobias Wunder / Moritz T Meyer / Nicky Atkinson / Antonio Martinez-Sanchez / Philip D Jeffrey / Sarah A Port / Weronika Patena / Guanhua He / ...Authors: Shan He / Hui-Ting Chou / Doreen Matthies / Tobias Wunder / Moritz T Meyer / Nicky Atkinson / Antonio Martinez-Sanchez / Philip D Jeffrey / Sarah A Port / Weronika Patena / Guanhua He / Vivian K Chen / Frederick M Hughson / Alistair J McCormick / Oliver Mueller-Cajar / Benjamin D Engel / Zhiheng Yu / Martin C Jonikas /
Abstract: Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO- ...Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.
History
DepositionJul 17, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateDec 23, 2020-
Current statusDec 23, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7jfo
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22308.png

Downloads & links

-
Map

FileDownload / File: emd_22308.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEPYC1(49-72) peptide-bound Rubisco. The map was processed at super resolution pixel size
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 251.52 Å		0.66 Å/pix.
x 384 pix.
= 251.52 Å		0.66 Å/pix.
x 384 pix.
= 251.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.655 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.04
Minimum - Maximum-0.4288977 - 0.6876844
Average (Standard dev.)-9.447558e-05 (±0.019309342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 251.51999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6550.6550.655
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z251.520251.520251.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.4290.688-0.000

-
Supplemental data

-
Additional map: EPYC1(49-72) peptide-bound Rubisco. The map was processed at...

Fileemd_22308_additional_1.map
AnnotationEPYC1(49-72) peptide-bound Rubisco. The map was processed at 2x binning of super resolution pixel size. The resolution reaches Nyquist frequency.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: EPYC1(49-72) peptide-bound Rubisco. The map was derived right...

Fileemd_22308_additional_2.map
AnnotationEPYC1(49-72) peptide-bound Rubisco. The map was derived right after 3DRefine at super resolution pixel size
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EPYC1(49-72) peptide-bound Rubisco

EntireName: EPYC1(49-72) peptide-bound Rubisco
Components
  • Complex: EPYC1(49-72) peptide-bound Rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
    • Protein or peptide: LCI5
  • Ligand: water

-
Supramolecule #1: EPYC1(49-72) peptide-bound Rubisco

SupramoleculeName: EPYC1(49-72) peptide-bound Rubisco / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

-
Macromolecule #1: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 52.607812 KDa
SequenceString: MVPQTETKAG AGFKAGVKDY RLTYYTPDYV VRDTDILAAF RMTPQPGVPP EECGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEP VPGEDNQYIA YVAYPIDLFE EGSVTNMFTS IVGNVFGFKA LRALRLEDLR IPPAYVKTFV GPPHGIQVER D KLNKYGRG ...String:
MVPQTETKAG AGFKAGVKDY RLTYYTPDYV VRDTDILAAF RMTPQPGVPP EECGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEP VPGEDNQYIA YVAYPIDLFE EGSVTNMFTS IVGNVFGFKA LRALRLEDLR IPPAYVKTFV GPPHGIQVER D KLNKYGRG LLGCTIKPKL GLSAKNYGRA VYECLRGGLD FTKDDENVNS QPFMRWRDRF LFVAEAIYKA QAETGEVKGH YL NATAGTC EEMMKRAV(SMC)A KELGVPIIMH DYLTGGFTAN TSLAIYCRDN GLLLHIHRAM HAVIDRQRNH GIHFRVLAK ALRMSGGDHL HSGTVVGKLE GEREVTLGFV DLMRDDYVEK DRSRGIYFTQ DWCSMPGVMP VASGGIHVWH MPALVEIFGD DACLQFGGG TLGHPWGNAP GAAANRVALE ACTQARNEGR DLAREGGDVI RSACKWSPEL AAACEVWKEI KFEFDTIDKL

-
Macromolecule #2: Ribulose bisphosphate carboxylase small chain 2, chloroplastic

MacromoleculeName: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 20.667959 KDa
SequenceString:
MAAVIAKSSV SAAVARPARS SVRPMAALKP AVKAAPVAAP AQANQMMVWT PVNNKMFETF SYLPPLSDEQ IAAQVDYIVA NGWIPCLEF AESDKAYVSN ESAIRFGSVS CLYYDNRYWT MWKLPMFGCR DPMQVLREIV ACTKAFPDAY VRLVAFDNQK Q VQIMGFLV QRPKSARDWQ PANKRSV

-
Macromolecule #3: LCI5

MacromoleculeName: LCI5 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 2.828148 KDa
SequenceString:
TNRVSPTRSV LPANWRQELE SLRN

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1198 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.8
Details: 200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2
GridModel: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
Details: glow discharging for 60 seconds with a current of 15 mA in a Pelico EasiGlow system.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7462 pixel / Digitization - Frames/image: 1-50 / Number real images: 2500 / Average exposure time: 10.0 sec. / Average electron dose: 58.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1809869
CTF correctionSoftware - Name: CTFFIND
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 945755
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1gk8

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7jfo:
EPYC1(49-72)-bound Rubisco

+
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