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- EMDB-19939: Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylp... -

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Basic information

Entry
Database: EMDB / ID: EMD-19939
TitleCryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site
Map datamain map
Sample
  • Complex: cytochrome b6f complex with decylplastoquinol bound at quinone reduction site
    • Protein or peptide: x 9 types
  • Ligand: x 10 types
Keywordsb6f complex / photosynthesis / membrane protein / electron transport / proton transport / quinone catalysis / water channels / OXIDOREDUCTASE
Function / homology
Function and homology information


PSII associated light-harvesting complex II binding / chloroplast photosystem I binding / chloroplast photosystem II binding / cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / thylakoid membrane / cytochrome complex assembly / photosynthetic electron transport chain ...PSII associated light-harvesting complex II binding / chloroplast photosystem I binding / chloroplast photosystem II binding / cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / thylakoid membrane / cytochrome complex assembly / photosynthetic electron transport chain / chloroplast thylakoid membrane / : / response to light stimulus / photosynthesis / chloroplast / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / lipid binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Thylakoid soluble phosphoprotein TSP9 / Thylakoid soluble phosphoprotein TSP9 superfamily / Thylakoid soluble phosphoprotein TSP9 / : / Cytochrome B6-F complex subunit VI (PetL) / 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 ...Thylakoid soluble phosphoprotein TSP9 / Thylakoid soluble phosphoprotein TSP9 superfamily / Thylakoid soluble phosphoprotein TSP9 / : / Cytochrome B6-F complex subunit VI (PetL) / 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 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 / Rudiment single hybrid motif / 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 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
Uncharacterized protein LOC110795548 / 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 / Thylakoid soluble phosphoprotein / Cytochrome b6-f complex subunit 6
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsPietras R / Pintscher S / Mielecki B / Szwalec M / Wojcik-Augustyn A / Indyka P / Rawski M / Koziej L / Jaciuk M / Wazny G ...Pietras R / Pintscher S / Mielecki B / Szwalec M / Wojcik-Augustyn A / Indyka P / Rawski M / Koziej L / Jaciuk M / Wazny G / Glatt S / Osyczka A
Funding support Poland, 3 items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-5B54/17-00 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
Polish National Science Centre2022/47/B/NZ1/03308 Poland
CitationJournal: Nat Plants / Year: 2024
Title: Molecular basis of plastoquinone reduction in plant cytochrome bf.
Authors: Sebastian Pintscher / Rafał Pietras / Bohun Mielecki / Mateusz Szwalec / Anna Wójcik-Augustyn / Paulina Indyka / Michał Rawski / Łukasz Koziej / Marcin Jaciuk / Grzegorz Ważny / ...Authors: Sebastian Pintscher / Rafał Pietras / Bohun Mielecki / Mateusz Szwalec / Anna Wójcik-Augustyn / Paulina Indyka / Michał Rawski / Łukasz Koziej / Marcin Jaciuk / Grzegorz Ważny / Sebastian Glatt / Artur Osyczka /
Abstract: A multi-subunit enzyme, cytochrome bf (cytbf), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone ...A multi-subunit enzyme, cytochrome bf (cytbf), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone (PQ) and plastocyanin. The atomic structure of cytbf is known, but its detailed catalytic mechanism remains elusive. Here we present cryogenic electron microscopy structures of spinach cytbf at 1.9 Å and 2.2 Å resolution, revealing an unexpected orientation of the substrate PQ in the haem ligand niche that forms the PQ reduction site (Q). PQ, unlike Q inhibitors, is not in direct contact with the haem. Instead, a water molecule is coordinated by one of the carbonyl groups of PQ and can act as the immediate proton donor for PQ. In addition, we identify water channels that connect Q with the aqueous exterior of the enzyme, suggesting that the binding of PQ in Q displaces water through these channels. The structures confirm large movements of the head domain of the iron-sulfur protein (ISP-HD) towards and away from the plastoquinol oxidation site (Q) and define the unique position of ISP-HD when a Q inhibitor (2,5-dibromo-3-methyl-6-isopropylbenzoquinone) is bound. This work identifies key conformational states of cytbf, highlights fundamental differences between substrates and inhibitors and proposes a quinone-water exchange mechanism.
History
DepositionMar 25, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19939.png

Downloads & links

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Map

FileDownload / File: emd_19939.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.095107555 - 0.32744175
Average (Standard dev.)0.000012505835 (±0.0039805006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19939_msk_1.map
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Mask #2

Fileemd_19939_msk_2.map
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Additional map: sharpened map

Fileemd_19939_additional_1.map
Annotationsharpened map
Projections & Slices
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Half map: half map B

Fileemd_19939_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_19939_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : cytochrome b6f complex with decylplastoquinol bound at quinone re...

EntireName: cytochrome b6f complex with decylplastoquinol bound at quinone reduction site
Components
  • Complex: cytochrome b6f complex with decylplastoquinol bound at quinone reduction site
    • Protein or peptide: Cytochrome b6
    • Protein or peptide: Cytochrome b6-f complex subunit 4
    • Protein or peptide: Cytochrome f
    • Protein or peptide: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
    • Protein or peptide: Cytochrome b6-f complex subunit 6
    • 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: Thylakoid soluble phosphoprotein
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: Decylplastoquinone
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL A
  • Ligand: UNDECYL-MALTOSIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: water

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Supramolecule #1: cytochrome b6f complex with decylplastoquinol bound at quinone re...

SupramoleculeName: cytochrome b6f complex with decylplastoquinol bound at quinone reduction site
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: cytochrome b6f complex incubated with reduced decyplastoquinone was mixed with plastocyanin and vitrified during turnover
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Cytochrome b6

MacromoleculeName: Cytochrome b6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 24.186504 KDa
SequenceString: MSKVYDWFEE RLEIQAIADD ITSKYVPPHV NIFYCLGGIT LTCFLVQVAT GFAMTFYYRP TVTDAFASVQ YIMTEVNFGW LIRSVHRWS ASMMVLMMIL HVFRVYLTGG FKKPRELTWV TGVVLGVLTA SFGVTGYSLP WDQIGYWAVK IVTGVPDAIP V IGSPLVEL ...String:
MSKVYDWFEE RLEIQAIADD ITSKYVPPHV NIFYCLGGIT LTCFLVQVAT GFAMTFYYRP TVTDAFASVQ YIMTEVNFGW LIRSVHRWS ASMMVLMMIL HVFRVYLTGG FKKPRELTWV TGVVLGVLTA SFGVTGYSLP WDQIGYWAVK IVTGVPDAIP V IGSPLVEL LRGSASVGQS TLTRFYSLHT FVLPLLTAVF MLMHFLMIRK QGISGPL

UniProtKB: Cytochrome b6

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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: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 17.456662 KDa
SequenceString:
MGVTKKPDLN DPVLRAKLAK GMGHNYYGEP AWPNDLLYIF PVVILGTIAC NVGLAVLEPS MIGEPADPFA TPLEILPEWY FFPVFQILR TVPNKLLGVL LMASVPAGLL TVPFLENVNK FQNPFRRPVA TTVFLVGTVV ALWLGIGATL PIDKSLTLGL F

UniProtKB: Cytochrome b6-f complex subunit 4

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Macromolecule #3: Cytochrome f

MacromoleculeName: Cytochrome f / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 35.355664 KDa
SequenceString: MQTINTFSWI KEQITRSISI SLILYIITRS SIANAYPIFA QQGYENPREA TGRIVCANCH LANKPVDIEV PQAVLPDTVF EAVVRIPYD MQLKQVLANG KKGGLNVGAV LILPEGFELA PPDRISPEMK EKMGNLSFQS YRPNKQNILV IGPVPGQKYS E ITFPILAP ...String:
MQTINTFSWI KEQITRSISI SLILYIITRS SIANAYPIFA QQGYENPREA TGRIVCANCH LANKPVDIEV PQAVLPDTVF EAVVRIPYD MQLKQVLANG KKGGLNVGAV LILPEGFELA PPDRISPEMK EKMGNLSFQS YRPNKQNILV IGPVPGQKYS E ITFPILAP DPATKKDVHF LKYPIYVGGN RGRGQIYPDG SKSNNTVYNS TATGIVKKIV RKEKGGYEIN IADASDGREV VD IIPRGPE LLVSEGESIK LDQPLTSNPN VGGFGQGDAE VVLQDPLRIQ GLLFFFASVI LAQIFLVLKK KQFEKVQLSE MNF

UniProtKB: Cytochrome f

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Macromolecule #4: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

MacromoleculeName: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: plastoquinol-plastocyanin reductase
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 24.347898 KDa
SequenceString: MASFTLSSAT PSQLCSSKNG MFAPSLALAK AGRVNVLISK ERIRGMKLTC QATSIPADNV PDMQKRETLN LLLLGALSLP TGYMLLPYA SFFVPPGGGA GTGGTIAKDA LGNDVIAAEW LKTHAPGDRT LTQGLKGDPT YLVVESDKTL ATFGINAVCT H LGCVVPFN ...String:
MASFTLSSAT PSQLCSSKNG MFAPSLALAK AGRVNVLISK ERIRGMKLTC QATSIPADNV PDMQKRETLN LLLLGALSLP TGYMLLPYA SFFVPPGGGA GTGGTIAKDA LGNDVIAAEW LKTHAPGDRT LTQGLKGDPT YLVVESDKTL ATFGINAVCT H LGCVVPFN AAENKFICPC HGSQYNNQGR VVRGPAPLSL ALAHCDVDDG KVVFVPWTET DFRTGEAPWW SA

UniProtKB: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

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Macromolecule #5: Cytochrome b6-f complex subunit 6

MacromoleculeName: Cytochrome b6-f complex subunit 6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 3.4522 KDa
SequenceString:
MFTLTSYFGF LLAALTITSA LFIGLNKIRL I

UniProtKB: Cytochrome b6-f complex subunit 6

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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: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 12.9538 KDa
SequenceString:
MATAAASTTL SSAAVPAISG SRGQRKMNKV VYMSGVNSYG GLKANNAVLG LGQAVCTEQC FANVVSSLRS TATKKGRSGG GGGAGGGAL TSTCNAAAEI FRIAAVMNGL TLVGVAIGFV LLRIEATVEE AE

UniProtKB: Uncharacterized protein LOC110795548

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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: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 4.171985 KDa
SequenceString:
MIEVFLFGIV LGLIPITLAG LFVTAYLQYR RGDQLDL

UniProtKB: Cytochrome b6-f complex subunit 5

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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: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 3.170809 KDa
SequenceString:
MDIVSLAWAA LMVVFTFSLS LVVWGRSGL

UniProtKB: Cytochrome b6-f complex subunit 8

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Macromolecule #9: Thylakoid soluble phosphoprotein

MacromoleculeName: Thylakoid soluble phosphoprotein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf
Molecular weightTheoretical: 10.608004 KDa
SequenceString:
MSSLPFVFGA AASSRVVTAA AAKGTAETKQ EKSFVDWLLG KITKEDQFYE TDPILRGGDV KSSGSTSGKK GGTTSGKKGT VSIPSKKKN GNGGVFGGLF AKKD

UniProtKB: Thylakoid soluble phosphoprotein

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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

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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

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Macromolecule #12: Decylplastoquinone

MacromoleculeName: Decylplastoquinone / type: ligand / ID: 12 / Number of copies: 2 / Formula: A1H65
Molecular weightTheoretical: 276.414 Da

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Macromolecule #13: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 13 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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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

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Macromolecule #15: UNDECYL-MALTOSIDE

MacromoleculeName: UNDECYL-MALTOSIDE / type: ligand / ID: 15 / Number of copies: 4 / Formula: UMQ
Molecular weightTheoretical: 496.589 Da
Chemical component information

ChemComp-UMQ:
UNDECYL-MALTOSIDE / detergent*YM

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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: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 17 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #18: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 18 / Number of copies: 2 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 214 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

Concentration5.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
50.0 mMNaClsodium chloride
1.0 mMC23H44O11n-undecyl beta-maltoside
0.5 mMC18H28O2decylplastoquinone
0.4 mMC18H30O2decylplastoquinonol
26.0 mMC2H6OSdimethyl sulfoxide
14.5 mMC2H5OHethanol

Details: final concentration of plastocyanin was 0.34 mM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsfinal concentration of cytochrome b6f dimers: 25uM

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4613 / Average electron dose: 40.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5580000 / Details: template picker, TOPAZ
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 482950
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.4.0) / Details: heterogenous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7zyv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9es8:
Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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