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- EMDB-14224: 2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP... -

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Basic information

Entry
Database: EMDB / ID: EMD-14224
Title2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules
Map data
Sample
  • Complex: Cytochrome b6f complex in association with PetP
    • Protein or peptide: x 9 types
  • Ligand: x 13 types
Function / homology
Function and homology information


: / cytochrome b6f complex / 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 / electron transfer activity ...: / cytochrome b6f complex / 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 / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Cytochrome b6f, subunit Tsr0524-like / Cytochrome b6f, subunit Tsr0524-like / 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 ...Cytochrome b6f, subunit Tsr0524-like / Cytochrome b6f, subunit Tsr0524-like / 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 / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rudiment single hybrid motif
Similarity search - Domain/homology
Uncharacterized protein Cp097, conserved in cyanobacteria / Cytochrome B6 / Cytochrome f / 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) / Synechocystis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFarmer DF / Proctor MS / Malone LA / Swainsbury DPK / Hawkings FR / Hitchcock A / Johnson MP
Funding support United Kingdom, 4 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
Wellcome Trustnr21005 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
DepositionFeb 2, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJul 27, 2022-
Current statusJul 27, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14224.png

Downloads & links

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Map

FileDownload / File: emd_14224.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.132
Minimum - Maximum-0.27047762 - 0.98646486
Average (Standard dev.)0.0046477783 (±0.035962984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14224_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_14224_half_map_2.map
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Sample components

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Entire : Cytochrome b6f complex in association with PetP

EntireName: Cytochrome b6f complex in association with PetP
Components
  • Complex: Cytochrome b6f complex in association with PetP
    • Protein or peptide: Uncharacterized protein Cp097, conserved in cyanobacteria
    • Protein or peptide: Cytochrome b6Cytochrome b
    • Protein or peptide: Cytochrome b6-f complex subunit 4
    • Protein or peptide: Cytochrome f
    • Protein or peptide: Cytochrome B6Cytochrome b
    • Protein or peptide: Cytochrome b6-f complex subunit 7
    • Protein or peptide: Cytochrome b6-f complex subunit 5
    • Protein or peptide: Cytochrome b6-f complex subunit 8
    • Protein or peptide: Rieske domain, PetC
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: beta,beta-caroten-4-one
  • Ligand: 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
  • Ligand: CHLOROPHYLL A
  • Ligand: HEME C
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: EICOSANEIcosane
  • Ligand: water

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Supramolecule #1: Cytochrome b6f complex in association with PetP

SupramoleculeName: Cytochrome b6f complex in association with PetP / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: strep-PetA used to purify cytochrome b6f complex from Synechocystis sp. PCC 6803. 6xHis-PetP recombinantly expressed in E. coli used to pull down cytochrome b6f complex and form the cytochrome b6f-PetP complex.
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Uncharacterized protein Cp097, conserved in cyanobacteria

MacromoleculeName: Uncharacterized protein Cp097, conserved in cyanobacteria
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis (bacteria) / Strain: PCC 6714
Molecular weightTheoretical: 7.231374 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MTIEIGQKVK VYRLRDRVSP DVVGKLGKVG VVKDFKMTDG SGIGAVVSFD DRTATWFFED ELKAI

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Macromolecule #2: Cytochrome b6

MacromoleculeName: Cytochrome b6 / 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: 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

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Macromolecule #3: Cytochrome b6-f complex subunit 4

MacromoleculeName: Cytochrome b6-f complex subunit 4 / 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: 17.455783 KDa
SequenceString:
MSIIKKPDLS DPDLRAKLAK GMGHNYYGEP AWPNDILYMF PICILGALGL IAGLAILDPA MIGEPADPFA TPLEILPEWY LYPTFQILR ILPNKLLGIA GMAAIPLGLM LVPFIESVNK FQNPFRRPIA MTVFLFGTAA ALWLGAGATF PIDKSLTLGL F

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Macromolecule #4: Cytochrome f

MacromoleculeName: Cytochrome f / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 35.25934 KDa
SequenceString: MRNPDTLGLW TKTMVALRRF TVLAIATVSV FLITDLGLPQ AASAYPFWAQ ETAPLTPREA TGRIVCANCH LAQKAAEVEI PQAVLPDTV FEAVVKIPYD LDSQQVLGDG SKGGLNVGAV LMLPEGFKIA PPDRLSEGLK EKVGGTYFQP YREDMENVVI V GPLPGEQY ...String:
MRNPDTLGLW TKTMVALRRF TVLAIATVSV FLITDLGLPQ AASAYPFWAQ ETAPLTPREA TGRIVCANCH LAQKAAEVEI PQAVLPDTV FEAVVKIPYD LDSQQVLGDG SKGGLNVGAV LMLPEGFKIA PPDRLSEGLK EKVGGTYFQP YREDMENVVI V GPLPGEQY QEIVFPVLSP DPAKDKSINY GKFAVHLGAN RGRGQIYPTG LLSNNNAFKA PNAGTISEVN ALEAGGYQLI LT TADGTET VDIPAGPELI VSAGQTVEAG EFLTNNPNVG GFGQKDTEVV LQNPTRIKFL VLFLAGIMLS QILLVLKKKQ IEK VQAAEL NF

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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

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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

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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: 4.177004 KDa
SequenceString:
MIEPLLLGIV LGLIPVTLAG LFVAAYLQYK RGNQFNLD

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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

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Macromolecule #9: Rieske domain, PetC

MacromoleculeName: Rieske domain, PetC / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 20.562344 KDa
SequenceString: MLVKILKFRR FIMTQISGSP DVPDLGRRQF MNLLTFGTIT GVAAGALYPA VKYLIPPSSG GSGGGVTAKD ALGNDVKVTE FLASHNAGD RVLAQGLKGD PTYIVVQGDD TIANYGINAV CTHLGCVVPW NASENKFMCP CHGSQYNAEG KVVRGPAPLS L ALAHATVT ...String:
MLVKILKFRR FIMTQISGSP DVPDLGRRQF MNLLTFGTIT GVAAGALYPA VKYLIPPSSG GSGGGVTAKD ALGNDVKVTE FLASHNAGD RVLAQGLKGD PTYIVVQGDD TIANYGINAV CTHLGCVVPW NASENKFMCP CHGSQYNAEG KVVRGPAPLS L ALAHATVT DDDKLVLSTW TETDFRTDED PWWA

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Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 10 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #11: (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: 11 / Number of copies: 4 / 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

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Macromolecule #12: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 12 / Number of copies: 2 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

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

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Macromolecule #13: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 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
type: ligand / ID: 13 / Number of copies: 2 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

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

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Macromolecule #14: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 14 / Number of copies: 2 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #15: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 15 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 16 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #17: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...

MacromoleculeName: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 17 / Number of copies: 2 / Formula: 6PL
Molecular weightTheoretical: 763.1 Da
Chemical component information

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 / phospholipid*YM

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Macromolecule #18: (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propa...

MacromoleculeName: (1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol
type: ligand / ID: 18 / Number of copies: 1 / Formula: 2WA
Molecular weightTheoretical: 570.927 Da
Chemical component information

ChemComp-2WA:
(1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol

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Macromolecule #19: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 19 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

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

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Macromolecule #20: 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: 20 / 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 #21: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 21 / Number of copies: 1 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE / Icosane

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Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 2 / 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 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
25.0 mLNa3PO4Sodium phosphate
10.0 mMMgCl2Magnesium chloride
150.0 mMNaClSodium chlorideSodium chloride
0.02 % (w/v)C56H92O25glyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 288 K / Instrument: LEICA EM GP
DetailsSample was monodisperse but not present in every hole

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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: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 20133 / Average exposure time: 3.5 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1169445
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14)
Startup modelType of model: INSILICO MODEL
Details: ab initio model generated from RELION's "initial model" job
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3.1)
Details: After initial 3D refinement; no alignment classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 152860
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ppw
PDB Unreleased entry

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7r0w:
2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules

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