7UNJ | pdb_00007unj

De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester matching geometry of purple bacterial special pair, SP1-ZnPPaM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.234 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 7UNJ

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 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.

Macromolecule Content 

  • Total Structure Weight: 51.29 kDa 
  • Atom Count: 3,373 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 446 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SP1-ZnPPaM designed chlorophyll dimer protein
A, B
223synthetic constructMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OE9
(Subject of Investigation/LOI)

Query on OE9



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
[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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.234 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.349α = 90
b = 52.349β = 90
c = 173.716γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



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)United StatesDE-AR0001543
Audacious Project at the Institute for Protein DesignUnited States68-2492: 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