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- EMDB-3951: Reaction centre light harvesting complex 1 from Blc. virids -

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Basic information

Entry
Database: EMDB / ID: EMD-3951
TitleReaction centre light harvesting complex 1 from Blc. virids
Map dataCryo-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.
Sample
  • Complex: Reaction centre-Light harvesting complex 1 (RC-LH1)
    • Protein or peptide: x 7 types
  • Ligand: x 10 types
Function / homology
Function and homology information


light-harvesting complex / organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis ...light-harvesting complex / organelle inner membrane / : / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / membrane => GO:0016020 / 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
Biological speciesBlastochloris viridis (bacteria) / Rhodopseudomonas viridis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsQian P / Siebert CA / Canniffe DP / Wang P / Hunter CN
Funding support1 items
OrganizationGrant numberCountry
European Research Council
CitationJournal: 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
DepositionOct 25, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseApr 11, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6et5
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3951.png

Downloads & links

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Map

FileDownload / File: emd_3951.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-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 sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0156 / Movie #1: 0.0156
Minimum - Maximum-0.020596072 - 0.080156974
Average (Standard dev.)0.0008213509 (±0.0040123253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 243.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z243.800243.800243.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0210.0800.001

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Supplemental data

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Half map: First half of map from last round of calculation Refine3D in RELION.

Fileemd_3951_half_map_1.map
AnnotationFirst half of map from last round of calculation Refine3D in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half of map from last round of calculation Refine3D in RELION.

Fileemd_3951_half_map_2.map
AnnotationSecond half of map from last round of calculation Refine3D in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Reaction centre-Light harvesting complex 1 (RC-LH1)

EntireName: Reaction centre-Light harvesting complex 1 (RC-LH1)
Components
  • Complex: Reaction centre-Light harvesting complex 1 (RC-LH1)
    • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
    • Protein or peptide: Reaction center protein L chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein H chainPhotosynthetic reaction centre
    • Protein or peptide: Light-harvesting protein B-1015 alpha chain
    • Protein or peptide: Light-harvesting protein B-1015 beta chain
    • Protein or peptide: Light-harvesting protein B-1015 gamma chain
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: BACTERIOCHLOROPHYLL B
  • Ligand: BACTERIOPHEOPHYTIN B
  • Ligand: Ubiquinone-9Coenzyme Q10
  • Ligand: FE (III) ION
  • Ligand: SULFATE IONSulfate
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: MENAQUINONE-9Vitamin K2
  • Ligand: 15-cis-1,2-dihydroneurosporene
  • Ligand: all-trans-1,2-dihydroneurosporene

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Supramolecule #1: Reaction centre-Light harvesting complex 1 (RC-LH1)

SupramoleculeName: Reaction centre-Light harvesting complex 1 (RC-LH1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: The protein was isolated from a photosynthetic bacterium Blc. viridis.
Source (natural)Organism: Blastochloris viridis (bacteria)
Molecular weightExperimental: 414 KDa

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Macromolecule #1: Photosynthetic reaction center cytochrome c subunit

MacromoleculeName: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 1 / Details: reaction centre cytochrome subunit / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 37.179465 KDa
SequenceString: CFEPPPATTT QTGFRGLSMG EVLHPATVKA KKERDAQYPP ALAAVKAEGP PVSQVYKNVK VLGNLTEAEF LRTMTAITEW VSPQEGCTY CHDENNLASE AKYPYVVARR MLEMTRAINT NWTQHVAQTG VTCYTCHRGT PLPPYVRYLE PTLPLNNRET P THVERVET ...String:
CFEPPPATTT QTGFRGLSMG EVLHPATVKA KKERDAQYPP ALAAVKAEGP PVSQVYKNVK VLGNLTEAEF LRTMTAITEW VSPQEGCTY CHDENNLASE AKYPYVVARR MLEMTRAINT NWTQHVAQTG VTCYTCHRGT PLPPYVRYLE PTLPLNNRET P THVERVET RSGYVVRLAK YTAYSALNYD PFTMFLANDK RQVRVVPQTA LPLVGVSRGK ERRPLSDAYA TFALMMSISD SL GTNCTFC HNAQTFESWG KKSTPQRAIA WWGIRMVRDL NMNYLAPLNA SLPASRLGRQ GEAPQADCRT CHQGVTKPLF GAS RLKDYP ELGPIKA

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Macromolecule #2: Reaction center protein L chain

MacromoleculeName: Reaction center protein L chain / type: protein_or_peptide / ID: 2 / Details: reaction centre L subunit / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 30.600299 KDa
SequenceString: MALLSFERKY RVRGGTLIGG DLFDFWVGPY FVGFFGVSAI FFIFLGVSLI GYAASQGPTW DPFAISINPP DLKYGLGAAP LLEGGFWQA ITVCALGAFI SWMLREVEIS RKLGIGWHVP LAFCVPIFMF CVLQVFRPLL LGSWGHAFPY GILSHLDWVN N FGYQYLNW ...String:
MALLSFERKY RVRGGTLIGG DLFDFWVGPY FVGFFGVSAI FFIFLGVSLI GYAASQGPTW DPFAISINPP DLKYGLGAAP LLEGGFWQA ITVCALGAFI SWMLREVEIS RKLGIGWHVP LAFCVPIFMF CVLQVFRPLL LGSWGHAFPY GILSHLDWVN N FGYQYLNW HYNPGHMSSV SFLFVNAMAL GLHGGLILSV ANPGDGDKVK TAEHENQYFR DVVGYSIGAL SIHRLGLFLA SN IFLTGAF GTIASGPFWT RGWPEWWGWW LDIPFWS

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Macromolecule #3: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 3 / Details: Teaction centre M subunit / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 35.932188 KDa
SequenceString: ADYQTIYTQI QARGPHITVS GEWGDNDRVG KPFYSYWLGK IGDAQIGPIY LGASGIAAFA FGSTAILIIL FNMAAEVHFD PLQFFRQFF WLGLYPPKAQ YGMGIPPLHD GGWWLMAGLF MTLSLGSWWI RVYSRARALG LGTHIAWNFA AAIFFVLCIG C IHPTLVGS ...String:
ADYQTIYTQI QARGPHITVS GEWGDNDRVG KPFYSYWLGK IGDAQIGPIY LGASGIAAFA FGSTAILIIL FNMAAEVHFD PLQFFRQFF WLGLYPPKAQ YGMGIPPLHD GGWWLMAGLF MTLSLGSWWI RVYSRARALG LGTHIAWNFA AAIFFVLCIG C IHPTLVGS WSEGVPFGIW PHIDWLTAFS IRYGNFYYCP WHGFSIGFAY GCGLLFAAHG ATILAVARFG GDREIEQITD RG TAVERAA LFWRWTIGFN ATIESVHRWG WFFSLMVMVS ASVGILLTGT FVDNWYLWCV KHGAAPDYPA YLPATPDPAS LPG APK

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Macromolecule #4: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 4 / Details: Reaction centre H subunit / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 28.557453 KDa
SequenceString: (FME)YHGALAQHL DIAQLVWYAQ WLVIWTVVLL YLRREDRREG YPLVEPLGLV KLAPEDGQVY ELPYPKTFVL PHGGTV TVP RRRPETRELK LAQTDGFEGA PLQPTGNPLV DAVGPASYAE RAEVVDATVD GKAKIVPLRV ATDFSIAEGD VDPRGLP VV AADGVEAGTV ...String:
(FME)YHGALAQHL DIAQLVWYAQ WLVIWTVVLL YLRREDRREG YPLVEPLGLV KLAPEDGQVY ELPYPKTFVL PHGGTV TVP RRRPETRELK LAQTDGFEGA PLQPTGNPLV DAVGPASYAE RAEVVDATVD GKAKIVPLRV ATDFSIAEGD VDPRGLP VV AADGVEAGTV TDLWVDRSEH YFRYLELSVA GSARTALIPL GFCDVKKDKI VVTSILSEQF ANVPRLQSRD QITLREED K VSAYYAGGLL YATPERAESL L

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Macromolecule #5: Light-harvesting protein B-1015 alpha chain

MacromoleculeName: Light-harvesting protein B-1015 alpha chain / type: protein_or_peptide / ID: 5 / Details: Light harvesting complex 1 alpha subunit / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 6.984262 KDa
SequenceString:
MATEYRTASW KLWLILDPRR VLTALFVYLT VIALLIHFGL LSTDRLNWWE FQRGLPKAA

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Macromolecule #6: Light-harvesting protein B-1015 beta chain

MacromoleculeName: Light-harvesting protein B-1015 beta chain / type: protein_or_peptide / ID: 6 / Details: Light harvesting complex 1 beta subunit / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 6.274327 KDa
SequenceString:
MADLKPSLTG LTEEEAKEFH GIFVTSTVLY LATAVIVHYL VWTARPWIAP IPKGWV

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Macromolecule #7: Light-harvesting protein B-1015 gamma chain

MacromoleculeName: Light-harvesting protein B-1015 gamma chain / type: protein_or_peptide / ID: 7 / Details: Light harvesting complex 1 gamma subunit / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas viridis (bacteria)
Molecular weightTheoretical: 2.799292 KDa
SequenceString:
SDWNLWVPLG ILGIPTIWIA LTYR

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Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 8 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #9: BACTERIOCHLOROPHYLL B

MacromoleculeName: BACTERIOCHLOROPHYLL B / type: ligand / ID: 9 / Number of copies: 38 / Formula: BCB
Molecular weightTheoretical: 909.488 Da
Chemical component information

ChemComp-BCB:
BACTERIOCHLOROPHYLL B / Bacteriochlorophyll

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Macromolecule #10: BACTERIOPHEOPHYTIN B

MacromoleculeName: BACTERIOPHEOPHYTIN B / type: ligand / ID: 10 / Number of copies: 2 / Formula: BPB
Molecular weightTheoretical: 887.199 Da
Chemical component information

ChemComp-BPB:
BACTERIOPHEOPHYTIN B / Pheophytin

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Macromolecule #11: Ubiquinone-9

MacromoleculeName: Ubiquinone-9 / type: ligand / ID: 11 / Number of copies: 2 / Formula: UQ9
Molecular weightTheoretical: 795.226 Da
Chemical component information

ChemComp-UQ9:
Ubiquinone-9

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Macromolecule #12: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #13: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 13 / Number of copies: 7 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION / Sulfate

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Macromolecule #14: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 14 / Number of copies: 2 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM / Lauryldimethylamine oxide

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Macromolecule #15: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 15 / Number of copies: 1 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9 / Vitamin K2

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Macromolecule #16: 15-cis-1,2-dihydroneurosporene

MacromoleculeName: 15-cis-1,2-dihydroneurosporene / type: ligand / ID: 16 / Number of copies: 1 / Formula: NS5
Molecular weightTheoretical: 540.904 Da
Chemical component information

ChemComp-NS5:
15-cis-1,2-dihydroneurosporene

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Macromolecule #17: all-trans-1,2-dihydroneurosporene

MacromoleculeName: all-trans-1,2-dihydroneurosporene / type: ligand / ID: 17 / Number of copies: 17 / Formula: NS0
Molecular weightTheoretical: 540.904 Da
Chemical component information

ChemComp-NS0:
all-trans-1,2-dihydroneurosporene

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration4.0 mg/mL
BufferpH: 7.8 / Component - Concentration: 20.0 mMol / Component - Name: HEPES / Details: 20 mMol HEPES, pH 7.8, 100 mM NaCl
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 278 K / Instrument: LEICA EM GP
Details: Blot for 3.5 seconds. Humidity: 99% Temperature:4C..
DetailsProtein 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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 267726 / Details: Protein was checked using negatively stained EM.
CTF correctionSoftware - Name: Gctf (ver. 1.06) / Details: gctf was used for CTF correction
Startup modelType of model: INSILICO MODEL
In silico model: EMAN2 was used for initial model creation by the use of 2d classes from relion 2d classification.
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN (ver. 2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.0)
Details: 166793 particles, 62.3% in total, were used for final 3D reconstruction
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 267726
DetailsDose fractioned
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6et5:
Reaction centre light harvesting complex 1 from Blc. virids

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