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- EMDB-13590: Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 c... -

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Basic information

Entry
Database: EMDB / ID: EMD-13590
TitleCryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation
Map datalight harvesting core complex
Sample
  • Complex: Light harvesting core complex
    • Protein or peptide: x 8 types
  • Ligand: x 11 types
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Reaction center protein M chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQian P / Hunter CN
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
European Research Council (ERC)845126 United Kingdom
Wellcome Trust209407/Z/17/Z United Kingdom
Citation
Journal: Biochem J / Year: 2021
Title: Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation.
Authors: Pu Qian / Tristan I Croll / Andrew Hitchcock / Philip J Jackson / Jack H Salisbury / Pablo Castro-Hartmann / Kasim Sader / David J K Swainsbury / C Neil Hunter /
Abstract: The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and ...The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and proton acceptor to a quinol. The angle between the two monomers imposes a bent configuration on the dimer complex, which exerts a major influence on the curvature of the membrane vesicles, known as chromatophores, where the light-driven photosynthetic reactions take place. To investigate the dimerisation interface between two RC-LH1 monomers, we determined the cryogenic electron microscopy structure of the dimeric complex at 2.9 Å resolution. The structure shows that each monomer consists of a central RC partly enclosed by a 14-subunit LH1 ring held in an open state by PufX and protein-Y polypeptides, thus enabling quinones to enter and leave the complex. Two monomers are brought together through N-terminal interactions between PufX polypeptides on the cytoplasmic side of the complex, augmented by two novel transmembrane polypeptides, designated protein-Z, that bind to the outer faces of the two central LH1 β polypeptides. The precise fit at the dimer interface, enabled by PufX and protein-Z, by C-terminal interactions between opposing LH1 αβ subunits, and by a series of interactions with a bound sulfoquinovosyl diacylglycerol lipid, bring together each monomer creating an S-shaped array of 28 bacteriochlorophylls. The seamless join between the two sets of LH1 bacteriochlorophylls provides a path for excitation energy absorbed by one half of the complex to migrate across the dimer interface to the other half.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Qian P / Hunter CN
History
DepositionSep 17, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBe / 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-7pqd
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13590.png

Downloads & links

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Map

FileDownload / File: emd_13590.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlight harvesting core complex
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.0222 / Movie #1: 0.03
Minimum - Maximum-0.11344796 - 0.21005328
Average (Standard dev.)0.00032892064 (±0.004754529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ260260260
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1130.2100.000

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Supplemental data

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Sample components

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Entire : Light harvesting core complex

EntireName: Light harvesting core complex
Components
  • Complex: Light harvesting core complex
    • Protein or peptide: LH1-alpha
    • Protein or peptide: LH1-beta
    • Protein or peptide: RC-H
    • Protein or peptide: RC-L
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: PufZ
    • Protein or peptide: PufY
    • Protein or peptide: PufX
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: 3,4-DIHYDROSPHEROIDENE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
  • Ligand: UBIQUINONE-1Coenzyme Q10
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Light harvesting core complex

SupramoleculeName: Light harvesting core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)

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Macromolecule #1: LH1-alpha

MacromoleculeName: LH1-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 6.84418 KDa
SequenceString:
(FME)SKFYKIWMI FDPRRVFVAQ GVFLFLLAVM IHLILLSTPS YNWLEISAAK YNRVAVAE

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Macromolecule #2: LH1-beta

MacromoleculeName: LH1-beta / type: protein_or_peptide / ID: 2 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 5.592361 KDa
SequenceString:
MADKSDLGYT GLTDEQAQEL HSVYMSGLWL FSAVAIVAHL AVYIWRPWF

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Macromolecule #3: RC-H

MacromoleculeName: RC-H / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 26.544471 KDa
SequenceString: MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FHVSAGKNPI GLPVRGCDLE I AGKVVDIW ...String:
MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FHVSAGKNPI GLPVRGCDLE I AGKVVDIW VDIPEQMARF LEVELKDGST RLLPMQMVKV QSNRVHVNAL SSDLFAGIPT IKSPTEVTLL EEDKICGYVA GG LMYAAP

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Macromolecule #4: RC-L

MacromoleculeName: RC-L / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 31.346389 KDa
SequenceString: ALLSFERKYR VPGGTLVGGN LFDFWVGPFY VGFFGVATFF FAALGIILIA WSAVLQGTWN PQLISVYPPA LEYGLGGAPL AKGGLWQII TICATGAFVS WALREVEICR KLGIGYHIPF AFAFAILAYL TLVLFRPVMM GAWGYAFPYG IWTHLDWVSN T GYTYGNFH ...String:
ALLSFERKYR VPGGTLVGGN LFDFWVGPFY VGFFGVATFF FAALGIILIA WSAVLQGTWN PQLISVYPPA LEYGLGGAPL AKGGLWQII TICATGAFVS WALREVEICR KLGIGYHIPF AFAFAILAYL TLVLFRPVMM GAWGYAFPYG IWTHLDWVSN T GYTYGNFH YNPAHMIAIS FFFTNALALA LHGALVLSAA NPEKGKEMRT PDHEDTFFRD LVGYSIGTLG IHRLGLLLSL SA VFFSALC MIITGTIWFD QWVDWWQWWV KLPWWANIPG GING

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Macromolecule #5: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 34.398543 KDa
SequenceString: AEYQNIFSQV QVRGPADLGM TEDVNLANRS GVGPFSTLLG WFGNAQLGPI YLGSLGVLSL FSGLMWFFTI GIWFWYQAGW NPAVFLRDL FFFSLEPPAP EYGLSFAAPL KEGGLWLIAS FFMFVAVWSW WGRTYLRAQA LGMGKHTAWA FLSAIWLWMV L GFIRPILM ...String:
AEYQNIFSQV QVRGPADLGM TEDVNLANRS GVGPFSTLLG WFGNAQLGPI YLGSLGVLSL FSGLMWFFTI GIWFWYQAGW NPAVFLRDL FFFSLEPPAP EYGLSFAAPL KEGGLWLIAS FFMFVAVWSW WGRTYLRAQA LGMGKHTAWA FLSAIWLWMV L GFIRPILM GSWSEAVPYG IFSHLDWTNN FSLVHGNLFY NPFHGLSIAF LYGSALLFAM HGATILAVSR FGGERELEQI AD RGTAAER AALFWRWTMG FNATMEGIHR WAIWMAVLVT LTGGIGILLS GTVVDNWYVW GQNHGMAPLN

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Macromolecule #6: PufZ

MacromoleculeName: PufZ / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 3.517323 KDa
SequenceString:
MAYMFGIIVF LAMLAVCWFG FMAAERQAGR L

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Macromolecule #7: PufY

MacromoleculeName: PufY / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 5.126067 KDa
SequenceString:
EVSEFAFRLM MAAVIFVGVG IMFAFAGGHW FVGLVVGGLV AAFFAATPN

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Macromolecule #8: PufX

MacromoleculeName: PufX / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Molecular weightTheoretical: 6.024157 KDa
SequenceString:
PKTNLRLWVA FQMMKGAGWA GGVFFGTLLL IGFFRVVGRM LPIQENQAPA PNITG

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Macromolecule #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 64 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #10: 3,4-DIHYDROSPHEROIDENE

MacromoleculeName: 3,4-DIHYDROSPHEROIDENE / type: ligand / ID: 10 / Number of copies: 54 / Formula: SP2
Molecular weightTheoretical: 570.93 Da
Chemical component information

ChemComp-SP2:
3,4-DIHYDROSPHEROIDENE

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Macromolecule #11: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 11 / Number of copies: 4 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #12: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

MacromoleculeName: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate
type: ligand / ID: 12 / Number of copies: 4 / Formula: CD4
Molecular weightTheoretical: 1.241633 KDa
Chemical component information

ChemComp-CD4:
(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate

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Macromolecule #13: UBIQUINONE-1

MacromoleculeName: UBIQUINONE-1 / type: ligand / ID: 13 / Number of copies: 2 / Formula: UQ1
Molecular weightTheoretical: 250.29 Da
Chemical component information

ChemComp-UQ1:
UBIQUINONE-1

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Macromolecule #14: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 14 / Number of copies: 4 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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Macromolecule #15: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 15 / Number of copies: 4 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

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Macromolecule #16: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 16 / Number of copies: 2 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #17: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 17 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #18: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 144 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration4.0 mg/mL
BufferpH: 7.8 / Component - Concentration: 20.0 mMol / Component - Formula: HEPES / Details: 20 mM HEPES, pH 7.8, 0.03% beta-DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Details: QF R1.2/1.3 300 mesh Cu grid.
DetailsIn 20 mM HEPES, pH 7.8, 0.03% beta-DDM buffer solution

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMax: 80.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5058 / Average exposure time: 12.21 sec. / Average electron dose: 45.36 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 223786
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7pil

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 58945
FSC plot (resolution estimation)

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