[English] 日本語
Yorodumi
- EMDB-15017: 3.15 Angstrom cryo-EM structure of the dimeric cytochrome b6f com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15017
Title3.15 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Synechocystis sp. PCC 6803 with natively bound plastoquinone and lipid molecules.
Map data
Sample
  • Complex: Cytochrome b6f with natively associated lipids and plastoquinone
    • Protein or peptide: x 5 types
  • Protein or peptide: x 3 types
  • Ligand: x 7 types
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 / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis ...: / 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 / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / oxidoreductase activity / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 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. / 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 / Rieske iron-sulphur protein / Rudiment single hybrid motif / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cyclic nucleotide-binding domain
Similarity search - Domain/homology
Cytochrome B6 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit 2 / Cytochrome b6-f complex subunit 4 / Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 7 / Cytochrome b6
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMalone LA / Procter MS / Farmer DF / Swainsbury DJK / Hawkings FR / Pastorelli F / Emrich-Mills TZ / Siebert A / Hunter CN / Hitchcock A / Johnson MP
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006630/1 United Kingdom
Leverhulme TrustRPG-2019-045 United Kingdom
CitationJournal: Biochem J / Year: 2022
Title: Cryo-EM structures of the Synechocystis sp. PCC 6803 cytochrome b6f complex with and without the regulatory PetP subunit.
Authors: Matthew S Proctor / Lorna A Malone / David A Farmer / David J K Swainsbury / Frederick R Hawkings / Federica Pastorelli / Thomas Z Emrich-Mills / C Alistair Siebert / C Neil Hunter / Matthew ...Authors: Matthew S Proctor / Lorna A Malone / David A Farmer / David J K Swainsbury / Frederick R Hawkings / Federica Pastorelli / Thomas Z Emrich-Mills / C Alistair Siebert / C Neil Hunter / Matthew P Johnson / Andrew Hitchcock /
Abstract: In oxygenic photosynthesis, the cytochrome b6f (cytb6f) complex links the linear electron transfer (LET) reactions occurring at photosystems I and II and generates a transmembrane proton gradient via ...In oxygenic photosynthesis, the cytochrome b6f (cytb6f) complex links the linear electron transfer (LET) reactions occurring at photosystems I and II and generates a transmembrane proton gradient via the Q-cycle. In addition to this central role in LET, cytb6f also participates in a range of processes including cyclic electron transfer (CET), state transitions and photosynthetic control. Many of the regulatory roles of cytb6f are facilitated by auxiliary proteins that differ depending upon the species, yet because of their weak and transient nature the structural details of these interactions remain unknown. An apparent key player in the regulatory balance between LET and CET in cyanobacteria is PetP, a ∼10 kDa protein that is also found in red algae but not in green algae and plants. Here, we used cryogenic electron microscopy to determine the structure of the Synechocystis sp. PCC 6803 cytb6f complex in the presence and absence of PetP. Our structures show that PetP interacts with the cytoplasmic side of cytb6f, displacing the C-terminus of the PetG subunit and shielding the C-terminus of cytochrome b6, which binds the heme cn cofactor that is suggested to mediate CET. The structures also highlight key differences in the mode of plastoquinone binding between cyanobacterial and plant cytb6f complexes, which we suggest may reflect the unique combination of photosynthetic and respiratory electron transfer in cyanobacterial thylakoid membranes. The structure of cytb6f from a model cyanobacterial species amenable to genetic engineering will enhance future site-directed mutagenesis studies of structure-function relationships in this crucial ET complex.
History
DepositionMay 23, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJul 27, 2022-
Current statusJul 27, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15017.png

Downloads & links

-
Map

FileDownload / File: emd_15017.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0221
Minimum - Maximum-0.1518897 - 0.2722909
Average (Standard dev.)0.00060020294 (±0.00653787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_15017_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15017_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cytochrome b6f with natively associated lipids and plastoquinone

EntireName: Cytochrome b6f with natively associated lipids and plastoquinone
Components
  • Complex: Cytochrome b6f with natively associated lipids and plastoquinone
    • Protein or peptide: Cytochrome b6Cytochrome b
    • Protein or peptide: Cytochrome b6-f complex iron-sulfur subunit 2
    • Protein or peptide: Cytochrome B6Cytochrome b
    • Protein or peptide: Cytochrome b6-f complex subunit 7
    • Protein or peptide: Cytochrome b6-f complex subunit 8
  • Protein or peptide: Cytochrome b6-f complex subunit 4
  • Protein or peptide: Cytochrome f
  • Protein or peptide: Cytochrome b6-f complex subunit 5
  • Ligand: beta,beta-caroten-4-one
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: CHLOROPHYLL A
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: EICOSANEIcosane
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

+
Supramolecule #1: Cytochrome b6f with natively associated lipids and plastoquinone

SupramoleculeName: Cytochrome b6f with natively associated lipids and plastoquinone
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1, #4-#6, #8
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

+
Macromolecule #1: Cytochrome b6

MacromoleculeName: Cytochrome b6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 25.075533 KDa
SequenceString: MFSKEVTESK VFQWFNDRLE VQAISDDIAS KYVPPHVNIF YCLGGLTLTC FLIQFATGFA MTFYYKPTVT EAFASVQYIM NEVNFGWLI RSIHRWSASM MVLMMILHVF RVYLTGGFKK PRELTWVVGV MLAVTTVTFG VTGYSLPWDQ VGYWAVKIVS G VPAAIPVV ...String:
MFSKEVTESK VFQWFNDRLE VQAISDDIAS KYVPPHVNIF YCLGGLTLTC FLIQFATGFA MTFYYKPTVT EAFASVQYIM NEVNFGWLI RSIHRWSASM MVLMMILHVF RVYLTGGFKK PRELTWVVGV MLAVTTVTFG VTGYSLPWDQ VGYWAVKIVS G VPAAIPVV GDQLVTLMRG SESVGQATLT RFYSLHTFVL PWAIAVLLLL HFLMIRKQGI SGPL

+
Macromolecule #2: Cytochrome b6-f complex subunit 4

MacromoleculeName: Cytochrome b6-f complex subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 17.455783 KDa
SequenceString:
MSIIKKPDLS DPDLRAKLAK GMGHNYYGEP AWPNDILYMF PICILGALGL IAGLAILDPA MIGEPADPFA TPLEILPEWY LYPTFQILR ILPNKLLGIA GMAAIPLGLM LVPFIESVNK FQNPFRRPIA MTVFLFGTAA ALWLGAGATF PIDKSLTLGL F

+
Macromolecule #3: Cytochrome f

MacromoleculeName: Cytochrome f / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 30.512734 KDa
SequenceString: YPFWAQETAP LTPREATGRI VCANCHLAQK AAEVEIPQAV LPDTVFEAVV KIPYDLDSQQ VLGDGSKGGL NVGAVLMLPE GFKIAPPDR LSEGLKEKVG GTYFQPYRED MENVVIVGPL PGEQYQEIVF PVLSPDPAKD KSINYGKFAV HLGANRGRGQ I YPTGLLSN ...String:
YPFWAQETAP LTPREATGRI VCANCHLAQK AAEVEIPQAV LPDTVFEAVV KIPYDLDSQQ VLGDGSKGGL NVGAVLMLPE GFKIAPPDR LSEGLKEKVG GTYFQPYRED MENVVIVGPL PGEQYQEIVF PVLSPDPAKD KSINYGKFAV HLGANRGRGQ I YPTGLLSN NNAFKAPNAG TISEVNALEA GGYQLILTTA DGTETVDIPA GPELIVSAGQ TVEAGEFLTN NPNVGGFGQK DT EVVLQNP TRIKFLVLFL AGIMLSQILL VLKKKQIEKV QAAELNF

+
Macromolecule #4: Cytochrome b6-f complex iron-sulfur subunit 2

MacromoleculeName: Cytochrome b6-f complex iron-sulfur subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: plastoquinol-plastocyanin reductase
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 19.012287 KDa
SequenceString:
MTQISGSPDV PDLGRRQFMN LLTFGTITGV AAGALYPAVK YLIPPSSGGS GGGVTAKDAL GNDVKVTEFL ASHNAGDRVL AQGLKGDPT YIVVQGDDTI ANYGINAVCT HLGCVVPWNA SENKFMCPCH GSQYNAEGKV VRGPAPLSLA LAHATVTDDD K LVLSTWTE TDFRTDEDPW WA

+
Macromolecule #5: Cytochrome B6

MacromoleculeName: Cytochrome B6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 3.376149 KDa
SequenceString:
MAAGVGIFIG YIAVFTGVTL GLLYGLRFVK LI

+
Macromolecule #6: Cytochrome b6-f complex subunit 7

MacromoleculeName: Cytochrome b6-f complex subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.827555 KDa
SequenceString:
MTAESMLANG AFIMIGLTLL GLAWGFVIIK LQGSEE

+
Macromolecule #7: Cytochrome b6-f complex subunit 5

MacromoleculeName: Cytochrome b6-f complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.061917 KDa
SequenceString:
MIEPLLLGIV LGLIPVTLAG LFVAAYLQYK RGNQFNL

+
Macromolecule #8: Cytochrome b6-f complex subunit 8

MacromoleculeName: Cytochrome b6-f complex subunit 8 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.328965 KDa
SequenceString:
MDILTLGWVS VLVLFTWSIS MVVWGRNGF

+
Macromolecule #9: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 9 / Number of copies: 2 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-ECH:
beta,beta-caroten-4-one / Echinenone

+
Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
Macromolecule #11: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 11 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

+
Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 2 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

+
Macromolecule #13: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 13 / Number of copies: 7 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #14: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 14 / Number of copies: 2 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE / Icosane

+
Macromolecule #15: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 15 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 413442
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more