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- EMDB-31483: Cryo-EM structure of cyanobacterial PBS(delete Lr) from Synechoco... -

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Basic information

Entry
Database: EMDB / ID: EMD-31483
TitleCryo-EM structure of cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002
Map data
Sample
  • Complex: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002
Function / homology
Function and homology information


Lyases / : / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Allophycocyanin alpha subunit / Allophycocyanin subunit alpha-B / Allophycocyanin subunit beta-18 / Allophycocyanin beta subunit / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE / C-phycocyanin subunit alpha / C-phycocyanin subunit beta / Phycobilisome 32.3 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7002 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZheng L / Zheng Z / Li X / Wang G / Zhang K / Wei P / Zhao J / Gao N
Funding support1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)
CitationJournal: Nat Commun / Year: 2021
Title: Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes.
Authors: Lvqin Zheng / Zhenggao Zheng / Xiying Li / Guopeng Wang / Kun Zhang / Peijun Wei / Jindong Zhao / Ning Gao /
Abstract: Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both ...Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both consisting of phycobiliproteins and linker proteins. Here we report the cryo-EM structures of PBS from two cyanobacterial species, Anabaena 7120 and Synechococcus 7002. Both PBS are hemidiscoidal in shape and share a common triangular core structure. While the Anabaena PBS has two additional hexamers in the core linked by the 4th linker domain of ApcE (L). The PBS structures predict that, compared with the PBS from red algae, the cyanobacterial PBS could have more direct routes for energy transfer to ApcD. Structure-based systematic mutagenesis analysis of the chromophore environment of ApcD and ApcF subunits reveals that aromatic residues are critical to excitation energy transfer (EET). The structures also suggest that the linker protein could actively participate in the process of EET in both rods and the cores. These results provide insights into the organization of chromophores and the mechanisms of EET within cyanobacterial PBS.
History
DepositionJun 26, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31483.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.052 Å
Density
Contour LevelBy AUTHOR: 0.0213 / Movie #1: 0.0213
Minimum - Maximum-0.09642292 - 0.12914051
Average (Standard dev.)0.00065174093 (±0.004523799)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 420.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.800420.800420.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0960.1290.001

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Supplemental data

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Sample components

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Entire : cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002

EntireName: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002
Components
  • Complex: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002

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Supramolecule #1: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002

SupramoleculeName: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechococcus sp. PCC 7002 (bacteria)

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70852

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