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- EMDB-40209: Chlorophyll-binding region of de novo-designed nanocage O32-15 -

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Basic information

Entry
Database: EMDB / ID: EMD-40209
TitleChlorophyll-binding region of de novo-designed nanocage O32-15
Map dataChlorophyll-binding region of de novo-designed nanocage O32-15
Sample
  • Complex: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
    • Protein or peptide: C3-comp_O32-15
    • Protein or peptide: C2-chlorophyll-comp_O32-15_ctermHis
Keywordsnanocage / helical repeats / chlorophyll-binding / octahedral symmetry / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsRedler RL / Ennist NM / Wang S / Baker D / Ekiert DC / Bhabha G
Funding support United States, 2 items
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 / Naia 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, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40209.png

Downloads & links

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Map

FileDownload / File: emd_40209.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChlorophyll-binding region of de novo-designed nanocage O32-15
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 364 pix.
= 391.664 Å		1.08 Å/pix.
x 364 pix.
= 391.664 Å		1.08 Å/pix.
x 364 pix.
= 391.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.0448966 - 1.4923174
Average (Standard dev.)-0.001435626 (±0.013611514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 391.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_40209_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_40209_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM

EntireName: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
Components
  • Complex: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
    • Protein or peptide: C3-comp_O32-15
    • Protein or peptide: C2-chlorophyll-comp_O32-15_ctermHis

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Supramolecule #1: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM

SupramoleculeName: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: C3-comp_O32-15

MacromoleculeName: C3-comp_O32-15 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: STKEKARQLA EEAKETAEKV GDPELIKLAE QASQEGDSEK AKAILLAAEA ARVAKEVGAP DLIRLARIAA RVGASEAAKA ILLAAEAARV AKEVGDPELE RLALLAAVLG DSEKAKAILL AAEAARVAKE VGDPELIKLA LEAAERGDSE KAKAILLAAE AARVAKEVGD ...String:
STKEKARQLA EEAKETAEKV GDPELIKLAE QASQEGDSEK AKAILLAAEA ARVAKEVGAP DLIRLARIAA RVGASEAAKA ILLAAEAARV AKEVGDPELE RLALLAAVLG DSEKAKAILL AAEAARVAKE VGDPELIKLA LEAAERGDSE KAKAILLAAE AARVAKEVGD PELIKLALEA ARRGDSEKAK AILLAAEAAR VAKEVGDPEL IKLALEAARR GDSRKAEAIL LAAEAARIAK EAGDPEARKK ALEAARRGDR ELATRILIEA LLRLLKKSTA ELKRATASLR AITEELKKNP SEDALVEHNR AIVEHNAIIV ENNRIIAMVL EAIVRAI

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Macromolecule #2: C2-chlorophyll-comp_O32-15_ctermHis

MacromoleculeName: C2-chlorophyll-comp_O32-15_ctermHis / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DEEFKFLATE AKMLITAAER LAGTDPRLQE MVALIKKELE QAERTFRNGD KSEAQRQLEF VLTAARAVMN VAAAANAAGT DPLLKAMVDA ILWRLKEAIR TFQNGDQEEA ETQLRFVLRA AIAVAVVAAA LVLAGTDPEL QEMVEQIKDL LISAFMAGAR GDKEKALTQL ...String:
DEEFKFLATE AKMLITAAER LAGTDPRLQE MVALIKKELE QAERTFRNGD KSEAQRQLEF VLTAARAVMN VAAAANAAGT DPLLKAMVDA ILWRLKEAIR TFQNGDQEEA ETQLRFVLRA AIAVAVVAAA LVLAGTDPEL QEMVEQIKDL LISAFMAGAR GDKEKALTQL LFVAWAAHAV AMIAAAANLA GTDPRLQQQV KEILEKLKEA IETFQKGDEE QAFRQLAEVL AEAALVALRA ALTNLEHHHH HH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Average exposure time: 2.0 sec. / Average electron dose: 49.99 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 359331
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0)
Details: Particles were symmetry-expanded and partial-signal-subtracted prior to final refinement (Local Refinement in Cryosparc). Resolution of 5.2A is median resolution from Local Resolution Estimation in Cryosparc.
Number images used: 2844504
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)

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