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- PDB-7pil: Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY mon... -

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Basic information

Entry
Database: PDB / ID: 7pil
TitleCryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
Components
  • (Light-harvesting protein B-875 ...) x 2
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Intrinsic membrane protein PufX
  • RC-Y
KeywordsPHOTOSYNTHESIS / Photosynthetic bacteria / light harvesting complex / Cryo-EM / RC-LH1 / RC-LH1-PufX / RC-LH1-PufX-Y
Function / homology
Function and homology information


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 / membrane / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / 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 / 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 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / Chem-CD4 / : / SPHEROIDENE / UBIQUINONE-10 / UBIQUINONE-1 / Intrinsic membrane protein PufX / Reaction center protein H chain ...1,2-Distearoyl-sn-glycerophosphoethanolamine / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / Chem-CD4 / : / SPHEROIDENE / UBIQUINONE-10 / UBIQUINONE-1 / Intrinsic membrane protein PufX / Reaction center protein H chain / Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 alpha chain / Reaction center protein L chain / Reaction center protein M chain / Uncharacterized protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsQian, P. / Hunter, C.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1, United Kingdom
European Research Council (ERC)854126 United Kingdom
Wellcome Trust209407/Z/17/Z. United Kingdom
Citation
Journal: Biochem J / Year: 2021
Title: Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5 Å.
Authors: Pu Qian / David J K Swainsbury / Tristan I Croll / Jack H Salisbury / Elizabeth C Martin / Philip J Jackson / Andrew Hitchcock / Pablo Castro-Hartmann / Kasim Sader / C Neil Hunter /
Abstract: Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed ...Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed RC where a succession of electron and proton transfers conserves the energy as a quinol, which is exported to the cytochrome bc1 complex. In some RC-LH1 variants quinols can diffuse through small pores in a fully circular, 16-subunit LH1 ring, while in others missing LH1 subunits create a gap for quinol export. We used cryogenic electron microscopy to obtain a 2.5 Å resolution structure of one such RC-LH1, a monomeric complex from Rhodobacter sphaeroides. The structure shows that the RC is partly enclosed by a 14-subunit LH1 ring in which each αβ heterodimer binds two bacteriochlorophylls and, unusually for currently reported complexes, two carotenoids rather than one. Although the extra carotenoids confer an advantage in terms of photoprotection and light harvesting, they could impede passage of quinones through small, transient pores in the LH1 ring, necessitating a mechanism to create a dedicated quinone channel. The structure shows that two transmembrane proteins play a part in stabilising an open ring structure; one of these components, the PufX polypeptide, is augmented by a hitherto undescribed protein subunit we designate as protein-Y, which lies against the transmembrane regions of the thirteenth and fourteenth LH1α polypeptides. Protein-Y prevents LH1 subunits 11-14 adjacent to the RC QB site from bending inwards towards the RC and, with PufX preventing complete encirclement of the RC, this pair of polypeptides ensures unhindered quinone diffusion.
#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, C.N.
#2: Journal: To Be Published
Title: Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
Authors: Qian, P. / Hunter, C.N.
History
DepositionAug 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
AA: Light-harvesting protein B-875 alpha chain
AB: Light-harvesting protein B-875 alpha chain
AC: Light-harvesting protein B-875 alpha chain
AD: Light-harvesting protein B-875 alpha chain
AE: Light-harvesting protein B-875 alpha chain
AF: Light-harvesting protein B-875 alpha chain
AG: Light-harvesting protein B-875 alpha chain
AH: Light-harvesting protein B-875 alpha chain
AI: Light-harvesting protein B-875 alpha chain
AJ: Light-harvesting protein B-875 alpha chain
AK: Light-harvesting protein B-875 alpha chain
AL: Light-harvesting protein B-875 alpha chain
AM: Light-harvesting protein B-875 alpha chain
AN: Light-harvesting protein B-875 alpha chain
BA: Light-harvesting protein B-875 beta chain
BB: Light-harvesting protein B-875 beta chain
BC: Light-harvesting protein B-875 beta chain
BD: Light-harvesting protein B-875 beta chain
BE: Light-harvesting protein B-875 beta chain
BF: Light-harvesting protein B-875 beta chain
BG: Light-harvesting protein B-875 beta chain
BH: Light-harvesting protein B-875 beta chain
BI: Light-harvesting protein B-875 beta chain
BJ: Light-harvesting protein B-875 beta chain
BK: Light-harvesting protein B-875 beta chain
BL: Light-harvesting protein B-875 beta chain
BM: Light-harvesting protein B-875 beta chain
BN: Light-harvesting protein B-875 beta chain
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
UU: RC-Y
X: Intrinsic membrane protein PufX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,890106
Polymers263,84333
Non-polymers54,04773
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Mass spectrometer confirms the assembly
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Light-harvesting protein B-875 ... , 2 types, 28 molecules AAABACADAEAFAGAHAIAJAKALAMANBABBBCBDBEBFBGBHBIBJBKBLBMBN

#1: Protein
Light-harvesting protein B-875 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6516.847 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
References: UniProt: Q3J1A4
#2: Protein/peptide
Light-harvesting protein B-875 beta chain / Antenna pigment protein beta chain / LH-3A


Mass: 4943.656 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
References: UniProt: Q3J1A3

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Reaction center protein ... , 3 types, 3 molecules HLM

#3: Protein Reaction center protein H chain / Photosynthetic reaction centre / Photosynthetic reaction center H subunit


Mass: 26544.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
References: UniProt: Q3J170
#4: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
References: UniProt: Q3J1A5
#5: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / References: UniProt: Q3J1A6

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Protein/peptide / Protein / Sugars , 3 types, 6 molecules UUX

#10: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#6: Protein/peptide RC-Y


Mass: 5126.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
References: UniProt: U5NME9
#7: Protein Intrinsic membrane protein PufX


Mass: 5980.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria)
Strain: ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.
References: UniProt: P13402

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Non-polymers , 9 types, 73 molecules

#8: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical...
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C41H60O
#11: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#12: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4
#15: Chemical 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 / tetramyristoyl-cardiolipin


Mass: 1241.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C65H126O17P2
#16: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Light harvesting complexLight-harvesting complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Buffer solutionpH: 7.8 / Details: 20 mM HEPES, pH 7.8 , 0.03% beta-DDM
Buffer componentConc.: 20 mMol / Formula: HEPES
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: in 0.03% beta-DDM detergent
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: QF R1.2/1.3 grid coated graphene oxide

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12.21 sec. / Electron dose: 44.94 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3180

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_4234refinement
PHENIXdev_4234refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1057624
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250613 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT

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