7YK5

Rubisco from Phaeodactylum tricornutum bound to PYCO1(452-592)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A linker protein from a red-type pyrenoid phase separates with Rubisco via oligomerizing sticker motifs.

Oh, Z.G.Ang, W.S.L.Poh, C.W.Lai, S.K.Sze, S.K.Li, H.Y.Bhushan, S.Wunder, T.Mueller-Cajar, O.

(2023) Proc Natl Acad Sci U S A 120: e2304833120-e2304833120

  • DOI: https://doi.org/10.1073/pnas.2304833120
  • Primary Citation of Related Structures:  
    7YK5

  • PubMed Abstract: 

    The slow kinetics and poor substrate specificity of the key photosynthetic CO 2 -fixing enzyme Rubisco have prompted the repeated evolution of Rubisco-containing biomolecular condensates known as pyrenoids in the majority of eukaryotic microalgae. Diatoms dominate marine photosynthesis, but the interactions underlying their pyrenoids are unknown. Here, we identify and characterize the Rubisco linker protein PYCO1 from Phaeodactylum tricornutum . PYCO1 is a tandem repeat protein containing prion-like domains that localizes to the pyrenoid. It undergoes homotypic liquid-liquid phase separation (LLPS) to form condensates that specifically partition diatom Rubisco. Saturation of PYCO1 condensates with Rubisco greatly reduces the mobility of droplet components. Cryo-electron microscopy and mutagenesis data revealed the sticker motifs required for homotypic and heterotypic phase separation. Our data indicate that the PYCO1-Rubisco network is cross-linked by PYCO1 stickers that oligomerize to bind to the small subunits lining the central solvent channel of the Rubisco holoenzyme. A second sticker motif binds to the large subunit. Pyrenoidal Rubisco condensates are highly diverse and tractable models of functional LLPS.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain
A, B, C, D, E
A, B, C, D, E, F, G, H
490Phaeodactylum tricornutumMutation(s): 0 
EC: 4.1.1.39
UniProt
Find proteins for Q9TK52 (Phaeodactylum tricornutum (strain CCAP 1055/1))
Explore Q9TK52 
Go to UniProtKB:  Q9TK52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9TK52
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional fusion protein
I, J, K, L, M
I, J, K, L, M, N, O, P
139Phaeodactylum tricornutumMutation(s): 0 
UniProt
Find proteins for A0T0E2 (Phaeodactylum tricornutum (strain CCAP 1055/1))
Explore A0T0E2 
Go to UniProtKB:  A0T0E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0T0E2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PYCO1 SSU binding motifQ [auth i],
R [auth k],
S [auth j],
T [auth l]
8Phaeodactylum tricornutumMutation(s): 0 
UniProt
Find proteins for B7GCF7 (Phaeodactylum tricornutum (strain CCAP 1055/1))
Explore B7GCF7 
Go to UniProtKB:  B7GCF7
Entity Groups  
UniProt GroupB7GCF7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PYCO1 LSU binding motif9Phaeodactylum tricornutumMutation(s): 0 
UniProt
Find proteins for B7GCF7 (Phaeodactylum tricornutum (strain CCAP 1055/1))
Explore B7GCF7 
Go to UniProtKB:  B7GCF7
Entity Groups  
UniProt GroupB7GCF7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  6 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
HLU
Query on HLU
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC6 H13 N O3LEU
HYP
Query on HYP
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
LYO
Query on LYO
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC6 H14 N2 O3LYS
M3L
Query on M3L
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeMOE2018-T2-2-059
Ministry of Education (MoE, Singapore)SingaporeMOE2019-T3-1-012

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release