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- EMDB-2821: Negative stain electron microscopy reconstruction of an intact Ph... -

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Basic information

Entry
Database: EMDB / ID: EMD-2821
TitleNegative stain electron microscopy reconstruction of an intact Phycobilisome.
Map dataNegative stain electron microscopy reconstruction of the intact Phycobilisome from Anabaena sp. strain PCC 7120.
Sample
  • Sample: Phycobilisome from Anabaena sp. strain PCC 7120.
  • Protein or peptide: Phycobilisome
Keywordslight-harvesting antennae / photosynthesis
Biological speciesAnabaena (bacteria)
Methodsingle particle reconstruction / Resolution: 21.0 Å
AuthorsChang L / Liu X / Li Y / Liu CC / Yang F / Zhao J / Sui SF
CitationJournal: Cell Res / Year: 2015
Title: Structural organization of an intact phycobilisome and its association with photosystem II.
Authors: Leifu Chang / Xianwei Liu / Yanbing Li / Cui-Cui Liu / Fan Yang / Jindong Zhao / Sen-Fang Sui /
Abstract: Phycobilisomes (PBSs) are light-harvesting antennae that transfer energy to photosynthetic reaction centers in cyanobacteria and red algae. PBSs are supermolecular complexes composed of ...Phycobilisomes (PBSs) are light-harvesting antennae that transfer energy to photosynthetic reaction centers in cyanobacteria and red algae. PBSs are supermolecular complexes composed of phycobiliproteins (PBPs) that bear chromophores for energy absorption and linker proteins. Although the structures of some individual components have been determined using crystallography, the three-dimensional structure of an entire PBS complex, which is critical for understanding the energy transfer mechanism, remains unknown. Here, we report the structures of an intact PBS and a PBS in complex with photosystem II (PSII) from Anabaena sp. strain PCC 7120 using single-particle electron microscopy in combination with biochemical and molecular analyses. In the PBS structure, all PBP trimers and the conserved linker protein domains were unambiguously located, and the global distribution of all chromophores was determined. We provide evidence that ApcE and ApcF are critical for the formation of a protrusion at the bottom of PBS, which plays an important role in mediating PBS interaction with PSII. Our results provide insights into the molecular architecture of an intact PBS at different assembly levels and provide the basis for understanding how the light energy absorbed by PBS is transferred to PSII.
History
DepositionNov 17, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseJun 3, 2015-
UpdateJun 17, 2015-
Current statusJun 17, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2821.jpg

Downloads & links

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Map

FileDownload / File: emd_2821.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain electron microscopy reconstruction of the intact Phycobilisome from Anabaena sp. strain PCC 7120.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.46 Å/pix.
x 180 pix.
= 802.8 Å		4.46 Å/pix.
x 180 pix.
= 802.8 Å		4.46 Å/pix.
x 180 pix.
= 802.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-10.72281265 - 14.158310889999999
Average (Standard dev.)0.03494628 (±0.81071824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 802.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.464.464.46
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z802.800802.800802.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-10.72314.1580.035

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Supplemental data

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Sample components

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Entire : Phycobilisome from Anabaena sp. strain PCC 7120.

EntireName: Phycobilisome from Anabaena sp. strain PCC 7120.
Components
  • Sample: Phycobilisome from Anabaena sp. strain PCC 7120.
  • Protein or peptide: Phycobilisome

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Supramolecule #1000: Phycobilisome from Anabaena sp. strain PCC 7120.

SupramoleculeName: Phycobilisome from Anabaena sp. strain PCC 7120. / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 6 MDa

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Macromolecule #1: Phycobilisome

MacromoleculeName: Phycobilisome / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Anabaena (bacteria)
Molecular weightTheoretical: 6 MDa

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Details: 0.8 M K/Na-PO4
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJun 6, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 32966

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Atomic model buiding 1

Initial modelPDB ID:

1b33

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

1jbo

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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