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- EMDB-40208: Backbone model of de novo-designed chlorophyll-binding nanocage O32-15 -

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Basic information

Entry
Database: EMDB / ID: EMD-40208
TitleBackbone model of de novo-designed chlorophyll-binding nanocage O32-15
Map dataBackbone model of de novo-designed chlorophyll-binding nanocage O32-15
Sample
  • Complex: Chlorophyll-binding nanocage O32-15 loaded with ZnPPaM
    • Protein or peptide: C3-comp_O32-15, polyalanine model
    • Protein or peptide: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
Keywordsnanocage / helical repeats / chlorophyll-binding / octahedral symmetry / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 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: To Be Published
Title: De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs
Authors: Ennist NM / Wang S / Kennedy MA / Curti M / Sutherland GA / Vasilev C / Redler RL / Maffeis V / Shareef S / Sica AV / Hua AS / Deshmukh AP / Moyer AP / Hicks DR / Swartz AZ / Cacho RA / Novy ...Authors: Ennist NM / Wang S / Kennedy MA / Curti M / Sutherland GA / Vasilev C / Redler RL / Maffeis V / Shareef S / Sica AV / Hua AS / Deshmukh AP / Moyer AP / Hicks DR / Swartz AZ / Cacho RA / Novy N / Bera AK / Kang A / Sankaran B / Johnson MP / Reppert M / Ekiert DC / Bhabha G / Stewart L / Caram JR / Stoddard BL / Romero E / Hunter CN / Baker D
History
DepositionMar 23, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40208.png

Downloads & links

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Map

FileDownload / File: emd_40208.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBackbone model of de novo-designed chlorophyll-binding nanocage O32-15
Voxel sizeX=Y=Z: 1.076 Å
Density
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.042963542 - 0.44251803
Average (Standard dev.)0.0041361395 (±0.038141657)
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_40208_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_40208_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, polyalanine model
    • Protein or peptide: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model

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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, polyalanine model

MacromoleculeName: C3-comp_O32-15, polyalanine model / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 35.889559 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSTKEKARQL AEEAKETAEK VGDPELIKLA EQASQEGDSE KAKAILLAAE AARVAKEVGA PDLIRLARIA ARVGASEAAK AILLAAEAA RVAKEVGDPE LERLALLAAV LGDSEKAKAI LLAAEAARVA KEVGDPELIK LALEAAERGD SEKAKAILLA A EAARVAKE ...String:
MSTKEKARQL AEEAKETAEK VGDPELIKLA EQASQEGDSE KAKAILLAAE AARVAKEVGA PDLIRLARIA ARVGASEAAK AILLAAEAA RVAKEVGDPE LERLALLAAV LGDSEKAKAI LLAAEAARVA KEVGDPELIK LALEAAERGD SEKAKAILLA A EAARVAKE VGDPELIKLA LEAARRGDSE KAKAILLAAE AARVAKEVGD PELIKLALEA ARRGDSRKAE AILLAAEAAR IA KEAGDPE ARKKALEAAR RGDRELATRI LIEALLRLLK KSTAELKRAT ASLRAITEEL KKNPSEDALV EHNRAIVEHN AII VENNRI IAMVLEAIVR AI

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Macromolecule #2: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model

MacromoleculeName: C2-chlorophyll-comp_O32-15_ctermHis, polyalanine model
type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 27.799957 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDEEFKFLAT EAKMLITAAE RLAGTDPRLQ EMVALIKKEL EQAERTFRNG DKSEAQRQLE FVLTAARAVM NVAAAANAAG TDPLLKAMV DAILWRLKEA IRTFQNGDQE EAETQLRFVL RAAIAVAVVA AALVLAGTDP ELQEMVEQIK DLLISAFMAG A RGDKEKAL ...String:
MDEEFKFLAT EAKMLITAAE RLAGTDPRLQ EMVALIKKEL EQAERTFRNG DKSEAQRQLE FVLTAARAVM NVAAAANAAG TDPLLKAMV DAILWRLKEA IRTFQNGDQE EAETQLRFVL RAAIAVAVVA AALVLAGTDP ELQEMVEQIK DLLISAFMAG A RGDKEKAL TQLLFVAWAA HAVAMIAAAA NLAGTDPRLQ QQVKEILEKL KEAIETFQKG DEEQAFRQLA EVLAEAALVA LR AALTNLE HHHHHH

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 359331
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 205014

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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