8BP7 | pdb_00008bp7

Citrate-bound hexamer of Synechococcus elongatus citrate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.280 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.229 (Depositor) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BP7

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Emergence of fractal geometries in the evolution of a metabolic enzyme.

Sendker, F.L.Lo, Y.K.Heimerl, T.Bohn, S.Persson, L.J.Mais, C.N.Sadowska, W.Paczia, N.Nussbaum, E.Del Carmen Sanchez Olmos, M.Forchhammer, K.Schindler, D.Erb, T.J.Benesch, J.L.P.Marklund, E.G.Bange, G.Schuller, J.M.Hochberg, G.K.A.

(2024) Nature 628: 894-900

  • DOI: https://doi.org/10.1038/s41586-024-07287-2
  • Primary Citation Related Structures: 
    8AN1, 8BEI, 8BP7, 8RJK, 8RJL

  • PubMed Abstract: 

    Fractals are patterns that are self-similar across multiple length-scales 1 . Macroscopic fractals are common in nature 2-4 ; however, so far, molecular assembly into fractals is restricted to synthetic systems 5-12 . Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.


  • Organizational Affiliation
    • Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 269.02 kDa 
  • Atom Count: 17,892 
  • Modeled Residue Count: 2,244 
  • Deposited Residue Count: 2,364 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Citrate synthase
A, B, C, D, E
A, B, C, D, E, F
394Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_0612
UniProt
Find proteins for Q31QM5 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31QM5 
Go to UniProtKB:  Q31QM5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31QM5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
(Subject of Investigation/LOI)

Query on CIT



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
H [auth A]
I [auth A]
M [auth B]
AA [auth F],
BA [auth F],
H [auth A],
I [auth A],
M [auth B],
P [auth C],
T [auth D],
W [auth E],
X [auth E]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
J [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
J [auth A],
K [auth B],
L [auth B],
O [auth C],
R [auth D],
S [auth D],
V [auth E],
Y [auth F],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
CA [auth F],
DA [auth F],
N [auth B],
Q [auth C],
U [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.280 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.229 (Depositor) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.46α = 90
b = 170.46β = 90
c = 545.44γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary