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- PDB-7jsx: EPYC1(106-135) peptide-bound Rubisco -

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Basic information

Entry
Database: PDB / ID: 7jsx
TitleEPYC1(106-135) peptide-bound Rubisco
Components
  • EPYC1
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small chain 2, chloroplastic
KeywordsPLANT PROTEIN / Lyase / Rubisco / Pyrenoid
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 / Uncharacterized protein / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.06 Å
AuthorsMatthies, D. / He, S. / Jonikas, M.C.
Funding support United States, Singapore, United Kingdom, 9items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1359682 United States
National Science Foundation (NSF, United States)MCB-1935444 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-GM-119137 United States
Howard Hughes Medical Institute (HHMI)55108535 United States
Ministry of Education (MoE, Singapore)MOE2018-T2-2-059 Singapore
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S015531/1 United Kingdom
Leverhulme TrustRPG-2017-402 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007276 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
DepositionAug 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22462
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
I: Ribulose bisphosphate carboxylase large chain
J: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
K: Ribulose bisphosphate carboxylase large chain
L: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
M: Ribulose bisphosphate carboxylase large chain
N: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
O: Ribulose bisphosphate carboxylase large chain
P: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
q: EPYC1
r: EPYC1
s: EPYC1
t: EPYC1
u: EPYC1
v: EPYC1
w: EPYC1
x: EPYC1


Theoretical massNumber of molelcules
Total (without water)612,56424
Polymers612,56424
Non-polymers00
Water20,5551141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52607.812 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A0A218N8A3, UniProt: P00877*PLUS, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain 2, chloroplastic / RuBisCO small subunit 2


Mass: 20667.959 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P08475, ribulose-bisphosphate carboxylase
#3: Protein/peptide
EPYC1


Mass: 3294.677 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DA85
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: EPYC1(106-135) peptide-bound Rubisco / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 6.8
Details: 200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow discharging for 60 seconds with a current of 15 mA in a Pelico EasiGlow system
Grid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Cs: 0 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.56 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 13727
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
11cryoSPARCinitial Euler assignment
12RELIONfinal Euler assignment
13cryoSPARCclassification
14RELIONclassification
15RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2257131
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152839 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1GK8

1gk8

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