- EMDB-3951: Reaction centre light harvesting complex 1 from Blc. virids -
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Basic information
Entry
Database: EMDB / ID: EMD-3951
Title
Reaction centre light harvesting complex 1 from Blc. virids
Map data
Cryo-EM images of Reaction centre-light harvesting complex 1 (RC-LH1) from Blc. viridis were processed using RELION 2.0. The 3D cryo-EM map was produced after Post-processing to 2.87 Angstrom.
light-harvesting complex / organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis ...light-harvesting complex / organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / membrane => GO:0016020 / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile. Similarity search - Domain/homology
Light-harvesting protein B-1015 alpha chain / Light-harvesting protein B-1015 beta chain / Light-harvesting protein B-1015 gamma chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit Similarity search - Component
Journal: Nature / Year: 2018 Title: Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å. Authors: Pu Qian / C Alistair Siebert / Peiyi Wang / Daniel P Canniffe / C Neil Hunter / Abstract: The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the ...The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the bacteriochlorophyll b-based LH1-RC complex from Blastochloris viridis that reveals the structural basis for absorption of infrared light and the molecular mechanism of quinone migration across the LH1 complex. The triple-ring LH1 complex comprises a circular array of 17 β-polypeptides sandwiched between 17 α- and 16 γ-polypeptides. Tight packing of the γ-apoproteins between β-polypeptides collectively interlocks and stabilizes the LH1 structure; this, together with the short Mg-Mg distances of bacteriochlorophyll b pairs, contributes to the large redshift of bacteriochlorophyll b absorption. The 'missing' 17th γ-polypeptide creates a pore in the LH1 ring, and an adjacent binding pocket provides a folding template for a quinone, Q , which adopts a compact, export-ready conformation before passage through the pore and eventual diffusion to the cytochrome bc complex.
History
Deposition
Oct 25, 2017
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Header (metadata) release
Dec 20, 2017
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Map release
Apr 11, 2018
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Update
Nov 25, 2020
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Current status
Nov 25, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
#262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1)
#29 - May 2002 Penicillin-binding Proteins similarity (1)
#95 - Nov 2007 Multidrug Resistance Transporters similarity (1)
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Map
File
Download / File: emd_3951.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Cryo-EM images of Reaction centre-light harvesting complex 1 (RC-LH1) from Blc. viridis were processed using RELION 2.0. The 3D cryo-EM map was produced after Post-processing to 2.87 Angstrom.
Voxel size
X=Y=Z: 1.06 Å
Density
Contour Level
By AUTHOR: 0.0156 / Movie #1: 0.0156
Minimum - Maximum
-0.020596072 - 0.080156974
Average (Standard dev.)
0.0008213509 (±0.0040123253)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
230
230
230
Spacing
230
230
230
Cell
A=B=C: 243.79999 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.06
1.06
1.06
M x/y/z
230
230
230
origin x/y/z
0.000
0.000
0.000
length x/y/z
243.800
243.800
243.800
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
230
230
230
D min/max/mean
-0.021
0.080
0.001
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Supplemental data
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Half map: First half of map from last round of calculation Refine3D in RELION.
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0002 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 278 K / Instrument: LEICA EM GP Details: Blot for 3.5 seconds. Humidity: 99% Temperature:4C..
Details
Protein was solubilised by the use detergent of beta-DDM. The protein particle therefore contains a detergent belt in its hydrophobic region.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Temperature
Min: 77.0 K
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number grids imaged: 3 / Number real images: 6472 / Average exposure time: 0.5 sec. / Average electron dose: 2.25 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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