7UNI

De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

De novo design of proteins housing excitonically coupled chlorophyll special pairs.

Ennist, N.M.Wang, S.Kennedy, M.A.Curti, M.Sutherland, G.A.Vasilev, C.Redler, R.L.Maffeis, V.Shareef, S.Sica, A.V.Hua, A.S.Deshmukh, A.P.Moyer, A.P.Hicks, D.R.Swartz, A.Z.Cacho, R.A.Novy, N.Bera, A.K.Kang, A.Sankaran, B.Johnson, M.P.Phadkule, A.Reppert, M.Ekiert, D.Bhabha, G.Stewart, L.Caram, J.R.Stoddard, B.L.Romero, E.Hunter, C.N.Baker, D.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01626-0
  • Primary Citation of Related Structures:  
    7UNH, 7UNI, 7UNJ, 8EVM, 8GLT

  • PubMed Abstract: 

    Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C 2 -symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.


  • Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, WA, USA. ennist@uw.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SP2-ZnPPaM designed chlorophyll dimer proteinA,
B [auth C],
C [auth B],
D
250synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OE9 (Subject of Investigation/LOI)
Query on OE9

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C],
L [auth B],
N [auth D]
[methyl 9-ethenyl-14-ethyl-3-(3-methoxy-3-oxopropyl)-4,8,13,18-tetramethyl-20-oxophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc
C36 H36 N4 O5 Zn
KSFOOHVZTTVNHW-PIFGRXHESA-M
PGE
Query on PGE

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.855α = 87.83
b = 54.961β = 84.06
c = 89.365γ = 69.45
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1762114
Advanced Research Projects Agency-Energy (ARPA-E)DE-AR0001543
Audacious Project at the Institute for Protein Design68-2492: Audacious GC5: Next-Generation Nanoengineering

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-06-12
    Changes: Database references