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- EMDB-6828: Cryo-EM structure of the RC-LH core complex from Roseiflexus cast... -

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Basic information

Entry
Database: EMDB / ID: EMD-6828
TitleCryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii
Map data
Sample
  • Complex: photosynthetic core complex
    • Protein or peptide: alpha
    • Protein or peptide: beta
    • Protein or peptide: LM
    • Protein or peptide: cytochrome c
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding / membrane / 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, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, L subunit / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Cytochrome subunit of photosynthetic reaction center / Reaction center protein L chain / Alpha subunit of light-harvesting 1 / Beta subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsXin YY / Shi Y / Niu TX / Wang QQ / Niu WQ / Huang XJ / Ding W / Blankenship RE / Xu XL / Sun F
CitationJournal: Nat Commun / Year: 2018
Title: Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote.
Authors: Yueyong Xin / Yang Shi / Tongxin Niu / Qingqiang Wang / Wanqiang Niu / Xiaojun Huang / Wei Ding / Lei Yang / Robert E Blankenship / Xiaoling Xu / Fei Sun /
Abstract: Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important ...Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC-LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery.
History
DepositionSep 27, 2017-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 2, 2018-
UpdateMay 2, 2018-
Current statusMay 2, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5yq7
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6828.png

Downloads & links

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Map

FileDownload / File: emd_6828.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 192 pix.
= 215.04 Å		1.12 Å/pix.
x 192 pix.
= 215.04 Å		1.12 Å/pix.
x 192 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.058336068 - 0.144149
Average (Standard dev.)0.00085138995 (±0.0071420637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 215.04001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z215.040215.040215.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0580.1440.001

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Supplemental data

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Sample components

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Entire : photosynthetic core complex

EntireName: photosynthetic core complex
Components
  • Complex: photosynthetic core complex
    • Protein or peptide: alpha
    • Protein or peptide: beta
    • Protein or peptide: LM
    • Protein or peptide: cytochrome c

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Supramolecule #1: photosynthetic core complex

SupramoleculeName: photosynthetic core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 330 KDa

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Macromolecule #1: alpha

MacromoleculeName: alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
SequenceString:
MKDRPFEFRT SVVVSTLLGL VMALLIHFVV LSSGAFNWLR AP

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Macromolecule #2: beta

MacromoleculeName: beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
SequenceString:
MTDKPQNDLV PDQWKPLFNN AQWLVHDIVV KTIYGGLIIA VIAHVLCWAW TPWIR

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Macromolecule #3: LM

MacromoleculeName: LM / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
SequenceString: MSAVPRALPL PSGETLPAEA ISSTGSQAAS AEVIPFSIIE EFYKRPGKTL AARFFGVDPF DFWIGRFYVG LFGAISIIGI ILGVAFYLYE GVVNEGTLNI LAMRIEPPPV SQGLNVDPAQ PGFFWFLTMV AATIAFVGWL LRQIDISLKL DMGMEVPIAF GAVVSSWITL ...String:
MSAVPRALPL PSGETLPAEA ISSTGSQAAS AEVIPFSIIE EFYKRPGKTL AARFFGVDPF DFWIGRFYVG LFGAISIIGI ILGVAFYLYE GVVNEGTLNI LAMRIEPPPV SQGLNVDPAQ PGFFWFLTMV AATIAFVGWL LRQIDISLKL DMGMEVPIAF GAVVSSWITL QWLRPIAMGA WGHGFPLGIT HHLDWVSNIG YQYYNFFYNP FHAIGITLLF ASTLFLHMHG SAVLSEAKRN ISDQNIHVFW RNILGYSIGE IGIHRVAFWT GAASVLFSNL CIFLSGTFVK DWNAFWGFWD KMPIWNGVGQ GALVAGLSLL GVGLVLGRGR ETPGPIDLHD EEYRDGLEGT IAKPPGHVGW MQRLLGEGQV GPIYVGLWGV ISFITFFASA FIILVDYGRQ VGWNPIIYLR EFWNLAVYPP PTEYGLSWNV PWDKGGAWLA ATFFLHISVL TWWARLYTRA KATGVGTQLA WGFASALSLY FVIYLFHPLA LGNWSAAPGH GFRAILDWTN YVSIHWGNFY YNPFHMLSIF FLLGSTLLLA MHGATIVATS KWKSEMEFTE MMAEGPGTQR AQLFWRWVMG WNANSYNIHI WAWWFAAFTA ITGAIGLFLS GTLVPDWYAW GETAKIVAPW PNPDWAQYVF R

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Macromolecule #4: cytochrome c

MacromoleculeName: cytochrome c / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
SequenceString: MIQQPPTLFP EITNTVRGRF YIVAGIISVV MAVASIAIFW WIFYTITPAP APPLQNPIYV NYTQEPTDYI SAESLAAMNA YIQANPQPQA VQVLKGMTTA QISAYMVAQV SGGLKVDCSY CHNIANFAQQ DGYPNAAKKV TARKMMLMSA DLNQNYTAKL PASVGGYQIT ...String:
MIQQPPTLFP EITNTVRGRF YIVAGIISVV MAVASIAIFW WIFYTITPAP APPLQNPIYV NYTQEPTDYI SAESLAAMNA YIQANPQPQA VQVLKGMTTA QISAYMVAQV SGGLKVDCSY CHNIANFAQQ DGYPNAAKKV TARKMMLMSA DLNQNYTAKL PASVGGYQIT CATCHNGKAA GLEPYPIEIM NTLPNDWRLP LELDYPGGLV VTGRKDVSNH EVEQNQFAMY HMNVSMGQGC TFCHNARYFP SYEIAQKNHS IIMLQMTKHI QETYVAPGGR IADGIMAGKS PSCWLCHQGA NIPPGAAKPG QVPAVLSSTP

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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: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 73661 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: The startup model was generated by EMAN2.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148618
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 7.5 degrees
Final angle assignmentType: PROJECTION MATCHING

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