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- PDB-8glt: Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 -

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Basic information

Entry
Database: PDB / ID: 8glt
TitleBackbone model of de novo-designed chlorophyll-binding nanocage O32-15
Components
  • C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
  • C3-comp_O32-15, polyalanine model
KeywordsDE NOVO PROTEIN / nanocage / helical repeats / chlorophyll-binding / octahedral symmetry
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsRedler, R.L. / Ennist, N.M. / Wang, S. / Baker, D. / Ekiert, D.C. / Bhabha, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U19AG065156-02 United States
Other private
CitationJournal: Nat Chem Biol / Year: 2024
Title: De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh ...Authors: Nathan M Ennist / Shunzhi Wang / Madison A Kennedy / Mariano Curti / George A Sutherland / Cvetelin Vasilev / Rachel L Redler / Valentin Maffeis / Saeed Shareef / Anthony V Sica / Ash Sueh Hua / Arundhati P Deshmukh / Adam P Moyer / Derrick R Hicks / Avi Z Swartz / Ralph A Cacho / Nathan Novy / Asim K Bera / Alex Kang / Banumathi Sankaran / Matthew P Johnson / Amala Phadkule / Mike Reppert / Damian Ekiert / Gira Bhabha / Lance Stewart / Justin R Caram / Barry L Stoddard / Elisabet Romero / C Neil Hunter / David Baker /
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 ...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-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.
History
DepositionMar 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: 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
Revision 1.2Jul 10, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: C3-comp_O32-15, polyalanine model
1: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
3: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
5: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
7: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
9: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
B: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
BA: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
BB: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
BC: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
BD: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
BE: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
BF: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
D: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
F: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
H: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
J: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
L: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
N: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
P: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
R: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
T: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
V: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
X: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
Z: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
2: C3-comp_O32-15, polyalanine model
4: C3-comp_O32-15, polyalanine model
6: C3-comp_O32-15, polyalanine model
8: C3-comp_O32-15, polyalanine model
A: C3-comp_O32-15, polyalanine model
AB: C3-comp_O32-15, polyalanine model
AC: C3-comp_O32-15, polyalanine model
AE: C3-comp_O32-15, polyalanine model
AF: C3-comp_O32-15, polyalanine model
AG: C3-comp_O32-15, polyalanine model
AH: C3-comp_O32-15, polyalanine model
C: C3-comp_O32-15, polyalanine model
E: C3-comp_O32-15, polyalanine model
G: C3-comp_O32-15, polyalanine model
I: C3-comp_O32-15, polyalanine model
K: C3-comp_O32-15, polyalanine model
M: C3-comp_O32-15, polyalanine model
O: C3-comp_O32-15, polyalanine model
Q: C3-comp_O32-15, polyalanine model
S: C3-comp_O32-15, polyalanine model
U: C3-comp_O32-15, polyalanine model
W: C3-comp_O32-15, polyalanine model
Y: C3-comp_O32-15, polyalanine model


Theoretical massNumber of molelcules
Total (without water)1,528,54848
Polymers1,528,54848
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
C3-comp_O32-15, polyalanine model


Mass: 35889.559 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein ...
C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model


Mass: 27799.957 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 49.99 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.16_3549refinement
PHENIX1.16_3549refinement
EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2Topazparticle selection
3Leginonimage acquisition
5cryoSPARC3CTF correction
8UCSF Chimera1.13model fitting
10cryoSPARC3initial Euler assignment
11cryoSPARC3final Euler assignment
13cryoSPARC33D reconstruction
14PHENIX1.16model refinement
15Coot0.8.9.1model refinement
CTF correctionDetails: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 359331
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205014 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 0 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001667872
ELECTRON MICROSCOPYf_angle_d0.30894512
ELECTRON MICROSCOPYf_chiral_restr0.02913176
ELECTRON MICROSCOPYf_plane_restr0.001813584
ELECTRON MICROSCOPYf_dihedral_angle_d2.487939936

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