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- PDB-6rqf: 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f comp... -

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Entry
Database: PDB / ID: 6rqf
Title3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
  • Cytochrome b6Cytochrome b
  • Cytochrome f
KeywordsPHOTOSYNTHESIS / Plastoquinol-plastocyanin oxido-reductase Cytochrome b6f Photosynthesis Electron transport
Function / homology
Function and homology information


plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / mitochondrial respiratory chain complex III / photosynthetic electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane ...plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / mitochondrial respiratory chain complex III / photosynthetic electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Cytochrome B6-F complex subunit VI (PetL) / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily ...Cytochrome B6-F complex subunit VI (PetL) / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rudiment single hybrid motif / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-6PL / BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-PGV / Chem-PL9 / Chem-SQD ...Chem-6PL / BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-PGV / Chem-PL9 / Chem-SQD / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome b6-f complex iron-sulfur subunit, chloroplastic / Cytochrome f / Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 6
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsMalone, L.A. / Qian, P. / Mayneord, G.E. / Hitchcock, A. / Farmer, D. / Thompson, R. / Swainsbury, D.J.K. / Ranson, N. / Hunter, C.N. / Johnson, M.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000265/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P002005/1 United Kingdom
Leverhulme TrustRPG-2016-161 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structure of the spinach cytochrome bf complex at 3.6 Å resolution.
Authors: Lorna A Malone / Pu Qian / Guy E Mayneord / Andrew Hitchcock / David A Farmer / Rebecca F Thompson / David J K Swainsbury / Neil A Ranson / C Neil Hunter / Matthew P Johnson /
Abstract: The cytochrome b f (cytb f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane ...The cytochrome b f (cytb f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane proton gradient for ATP synthesis. Electron transfer within cytb f occurs via the quinol (Q) cycle, which catalyses the oxidation of plastoquinol (PQH) and the reduction of both plastocyanin (PC) and plastoquinone (PQ) at two separate sites via electron bifurcation. In higher plants, cytb f also acts as a redox-sensing hub, pivotal to the regulation of light harvesting and cyclic electron transfer that protect against metabolic and environmental stresses. Here we present a 3.6 Å resolution cryo-electron microscopy (cryo-EM) structure of the dimeric cytb f complex from spinach, which reveals the structural basis for operation of the Q cycle and its redox-sensing function. The complex contains up to three natively bound PQ molecules. The first, PQ1, is located in one cytb f monomer near the PQ oxidation site (Q) adjacent to haem b and chlorophyll a. Two conformations of the chlorophyll a phytyl tail were resolved, one that prevents access to the Q site and another that permits it, supporting a gating function for the chlorophyll a involved in redox sensing. PQ2 straddles the intermonomer cavity, partially obstructing the PQ reduction site (Q) on the PQ1 side and committing the electron transfer network to turnover at the occupied Q site in the neighbouring monomer. A conformational switch involving the haem c propionate promotes two-electron, two-proton reduction at the Q site and avoids formation of the reactive intermediate semiquinone. The location of a tentatively assigned third PQ molecule is consistent with a transition between the Q and Q sites in opposite monomers during the Q cycle. The spinach cytb f structure therefore provides new insights into how the complex fulfils its catalytic and regulatory roles in photosynthesis.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
I: Cytochrome b6
J: Cytochrome b6-f complex subunit 4
K: Cytochrome f
L: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
M: Cytochrome b6-f complex subunit 6
N: Cytochrome b6-f complex subunit 7
O: Cytochrome b6-f complex subunit 5
P: Cytochrome b6-f complex subunit 8
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Cytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,69745
Polymers213,05216
Non-polymers19,64529
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area91930 Å2
ΔGint-920 kcal/mol
Surface area81120 Å2
MethodPISA

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Components

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Protein , 3 types, 6 molecules IAKCLD

#1: Protein Cytochrome b6 / Cytochrome b


Mass: 24186.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00165
#3: Protein Cytochrome f /


Mass: 31357.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P16013
#4: Protein Cytochrome b6-f complex iron-sulfur subunit, chloroplastic / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / Rieske iron-sulfur protein / RISP


Mass: 18956.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P08980, plastoquinol-plastocyanin reductase

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Cytochrome b6-f complex subunit ... , 5 types, 10 molecules JBMENFOGPH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17456.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00166
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit PetL / Cytochrome b6-f complex subunit VI


Mass: 3452.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3L0
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit PetM / Cytochrome b6-f complex subunit VII


Mass: 3774.431 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P80883
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit PetG / Cytochrome b6-f complex subunit V


Mass: 4171.985 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69461
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit PetN / Cytochrome b6-f complex subunit VIII


Mass: 3170.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P61045

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Non-polymers , 10 types, 29 molecules

#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Chemical ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#12: Chemical ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#13: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C53H80O2
#14: Chemical ChemComp-6PL / (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 763.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#15: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#16: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#17: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#18: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78O12S

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Details

Has ligand of interestN

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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: Spinach Cytochrome b6f complex with native bound plastoquinone and thylakoid lipids
Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281 K

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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: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.15 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: (1.14_3260: phenix.real_space_refine) / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION2.1CTF correction
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 422660
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108560 / Symmetry type: POINT

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