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- EMDB-43843: Cryo-EM structure of a photosystem I variant containing an unusua... -

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Basic information

Entry
Database: EMDB / ID: EMD-43843
TitleCryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain
Map dataunsharpened and unmasked map
Sample
  • Complex: MenB Photosystem I
    • Protein or peptide: x 11 types
  • Ligand: x 16 types
Keywordscyanobacteria / photosystem I / MenB / phylloquinone / plastoquinone / benzoquinone / naphthoquinone / redox potential / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK 2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsGisriel CJ / Vasily K / Iwig DF / Russell BP / Vinyard DJ / Golbeck JH / Brudvig GW / Lakshmi KV
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
Department of Energy (DOE, United States)DE-FG02-07ER15903 United States
Department of Energy (DOE, United States)DE-SC0010575 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
Department of Energy (DOE, United States)DE-SC0020119 United States
CitationJournal: Sci Adv / Year: 2024
Title: Cryo-EM structure of a photosystem I variant containing an unusual plastoquinone derivative in its electron transfer chain.
Authors: Christopher J Gisriel / Vasily Kurashov / David F Iwig / Brandon P Russell / David J Vinyard / Gary W Brudvig / John H Golbeck / K V Lakshmi /
Abstract: Photosystem I (PS I) is a light-driven oxidoreductase responsible for converting photons into chemical bond energy. Its application for renewable energy was revolutionized by the creation of the MenB ...Photosystem I (PS I) is a light-driven oxidoreductase responsible for converting photons into chemical bond energy. Its application for renewable energy was revolutionized by the creation of the MenB deletion (Δ) variant in the cyanobacterium sp. PCC 6803, in which phylloquinone is replaced by plastoquinone-9 with a low binding affinity. This permits its exchange with exogenous quinones covalently coupled to dihydrogen catalysts that bind with high affinity, thereby converting PS I into a stable solar fuel catalyst. Here, we reveal the 2.03-Å-resolution cryo-EM structure of a recent MenB variant of PS I. The quinones and their binding environment are analyzed in the context of previous biophysical data, thereby enabling a protocol to solve future PS I hybrids and constructs from this genetically tractable cyanobacterium.
History
DepositionFeb 28, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43843.png

Downloads & links

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Map

FileDownload / File: emd_43843.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened and unmasked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0149
Minimum - Maximum-21.825500000000002 - 59.972029999999997
Average (Standard dev.)0.0014400833 (±1.0002513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened and unmasked map

Fileemd_43843_additional_1.map
Annotationunsharpened and unmasked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_43843_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_43843_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MenB Photosystem I

EntireName: MenB Photosystem I
Components
  • Complex: MenB Photosystem I
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK 2
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A
  • Ligand: 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: beta,beta-carotene-4,4'-dione
  • Ligand: CHLORIDE ION
  • Ligand: beta,beta-caroten-4-one
  • Ligand: CALCIUM ION
  • Ligand: (3'R)-3'-hydroxy-beta,beta-caroten-4-one
  • Ligand: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: MenB Photosystem I

SupramoleculeName: MenB Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 83.036398 KDa
SequenceString: MTISPPEREA KAKVSVDNNP VPTSFEKWGK PGHFDRTLAR GPKTTTWIWN LHANAHDFDS QTSDLEDVSR KIFSAHFGHL AVVFVWLSG MYFHGAKFSN YEGWLADPTH IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFYLWRA SGFTDSYQLY C TAIGGLVM ...String:
MTISPPEREA KAKVSVDNNP VPTSFEKWGK PGHFDRTLAR GPKTTTWIWN LHANAHDFDS QTSDLEDVSR KIFSAHFGHL AVVFVWLSG MYFHGAKFSN YEGWLADPTH IKPSAQVVWP IVGQGILNGD VGGGFHGIQI TSGLFYLWRA SGFTDSYQLY C TAIGGLVM AALMLFAGWF HYHVKAPKLE WFQNVESMMN HHLAGLLGLG SLGWAGHQIH VSMPINKLLD AGVAPKDIPL PH EFILEPS KMAELYPSFA QGLTPFFTLN WGVYSDFLTF KGGLNPVTGG LWLSDTAHHH LAIAVLFIIA GHMYRTNWGI GHS MKEILE AHKGPFTGEG HKGLYEILTT SWHAQLAINL ALLGSLTIIV AQHMYAMPPY PYQAIDYATQ LSLFTHHMWI GGFL IVGAG AHGAIFMVRD YDPAKNVNNL LDRMLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMRALG RPQDMFSDTA IQLQP IFAQ WVQHLHTLAP GATAPNALAT ASYAFGGETI AVAGKVAMMP ITLGTADFMV HHIHAFTIHV TALILLKGVL YARSSR LVP DKANLGFRFP CDGPGRGGTC QVSGWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVSP DGSVTHVTLG NFAQSAI TI NGWLRDFLWA QAANVINSYG SALSAYGIMF LAGHFVFAFS LMFLFSGRGY WQELIESIVW AHNKLNVAPA IQPRALSI I QGRAVGVAHY LLGGIVTTWA FFLARSLSIG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 81.298453 KDa
SequenceString: MTKFPKFSQD LAQDPTTRRI WYGIATAHDF ETHDGMTEEN LYQKIFASHF GHIAIIFLWT SGTLFHVAWQ GNFEQWIKDP LNIRPIAHA IWDPHFGEGA VNAFTQAGAS NPVNIAYSGV YHWFYTIGMT TNQELYSGAV FLLVLASLFL FAGWLHLQPK F RPSLAWFK ...String:
MTKFPKFSQD LAQDPTTRRI WYGIATAHDF ETHDGMTEEN LYQKIFASHF GHIAIIFLWT SGTLFHVAWQ GNFEQWIKDP LNIRPIAHA IWDPHFGEGA VNAFTQAGAS NPVNIAYSGV YHWFYTIGMT TNQELYSGAV FLLVLASLFL FAGWLHLQPK F RPSLAWFK NAESRLNHHL AGLFGVSSLA WAGHLVHVAI PEARGQHVGW DNFLSTPPHP AGLMPFFTGN WGVYAADPDT AG HIFGTSE GAGTAILTFL GGFHPQTESL WLTDIAHHHL AIAVIFIIAG HMYRTNWGIG HSIKEILNAH KGPLTGAGHT NLY DTINNS LHFQLGLALA SLGVITSLVA QHMYSLPSYA FIAQDHTTQA ALYTHHQYIA GFLMVGAFAH GAIFFVRDYD PVAN KDNVL ARMLEHKEAL ISHLSWVSLF LGFHTLGLYV HNDVVVAFGT PEKQILIEPV FAQWIQATSG KALYGFDVLL SNPDS IAST TGAAWLPGWL DAINSGTNSL FLTIGPGDFL VHHAIALGLH TTALILIKGA LDARGSKLMP DKKDFGYSFP CDGPGR GGT CDISAWDAFY LAMFWMLNTL GWLTFYWHWK HLGVWSGNVA QFNENSTYLM GWFRDYLWAN SAQLINGYNP YGVNNLS VW AWMFLFGHLV WATGFMFLIS WRGYWQELIE TIVWAHERTP LANLVRWKDK PVALSIVQAR LVGLAHFTVG YVLTYAAF L IASTAGKFG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 8.837261 KDa
SequenceString:
MSHSVKIYDT CIGCTQCVRA CPLDVLEMVP WDGCKAAQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 15.663749 KDa
SequenceString:
MTELSGQPPK FGGSTGGLLS KANREEKYAI TWTSASEQVF EMPTGGAAIM NEGENLLYLA RKEQCLALGT QLRTKFKPKI QDYKIYRVY PSGEVQYLHP ADGVFPEKVN EGREAQGTKT RRIGQNPEPV TIKFSGKAPY EV

UniProtKB: Photosystem I reaction center subunit II

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 8.154086 KDa
SequenceString:
MALNRGDKVR IKRTESYWYG DVGTVASVEK SGILYPVIVR FDRVNYNGFS GSASGVNTNN FAENELELVQ AAAK

UniProtKB: Photosystem I reaction center subunit IV

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Macromolecule #6: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 18.267082 KDa
SequenceString:
MKHLLALLLA FTLWFNFAPS ASADDFANLT PCSENPAYLA KSKNFLNTTN DPNSGKIRAE RYASALCGPE GYPHLIVDGR FTHAGDFLI PSILFLYIAG WIGWVGRSYL IEIRESKNPE MQEVVINVPL AIKKMLGGFL WPLAAVGEYT SGKLVMKDSE I PTSPR

UniProtKB: Photosystem I reaction center subunit III

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Macromolecule #7: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 4.414148 KDa
SequenceString:
MDGSYAASYL PWILIPMVGW LFPAVTMGLL FIHIESEGEG

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #8: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 4.535415 KDa
SequenceString:
MDGLKSFLST APVMIMALLT FTAGILIEFN RFYPDLLFHP

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit PsaK 2

MacromoleculeName: Photosystem I reaction center subunit PsaK 2 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 9.312122 KDa
SequenceString:
MFNTALLLAQ ASPTTAGWSL SVGIIMCLCN VFAFVIGYFA IQKTGKGKDL ALPQLASKKT FGLPELLATM SFGHILGAGM VLGLASSGI L

UniProtKB: Photosystem I reaction center subunit PsaK 2

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 16.631795 KDa
SequenceString:
MAESNQVVQA YNGDPFVGHL STPISDSAFT RTFIGNLPAY RKGLSPILRG LEVGMAHGYF LIGPWTLLGP LRDSEYQYIG GLIGALALI LVATAALSSY GLVTFQGEQG SGDTLQTADG WSQFAAGFFV GGMGGAFVAY FLLENLSVVD GIFRGLFN

UniProtKB: Photosystem I reaction center subunit XI

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Macromolecule #11: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 3.382063 KDa
SequenceString:
MALSDTQILA ALVVALLPAF LAFRLSTELY K

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 282 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #13: 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-y...

MacromoleculeName: 2,3-dimethyl-5-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione
type: ligand / ID: 13 / Number of copies: 6 / Formula: A1AGD
Molecular weightTheoretical: 414.664 Da

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 45 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 12 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #17: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 17 / Number of copies: 9 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #18: beta,beta-carotene-4,4'-dione

MacromoleculeName: beta,beta-carotene-4,4'-dione / type: ligand / ID: 18 / Number of copies: 3 / Formula: 45D
Molecular weightTheoretical: 564.84 Da
Chemical component information

ChemComp-45D:
beta,beta-carotene-4,4'-dione

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Macromolecule #19: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 19 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #20: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 20 / Number of copies: 6 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

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

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Macromolecule #21: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 21 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #22: (3'R)-3'-hydroxy-beta,beta-caroten-4-one

MacromoleculeName: (3'R)-3'-hydroxy-beta,beta-caroten-4-one / type: ligand / ID: 22 / Number of copies: 3 / Formula: EQ3
Molecular weightTheoretical: 566.856 Da
Chemical component information

ChemComp-EQ3:
(3'R)-3'-hydroxy-beta,beta-caroten-4-one

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Macromolecule #23: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,...

MacromoleculeName: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
type: ligand / ID: 23 / Number of copies: 6 / Formula: ZEX
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-ZEX:
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol

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Macromolecule #24: 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: 24 / Number of copies: 6 / 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 #25: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 25 / Number of copies: 3 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #26: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 26 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #27: water

MacromoleculeName: water / type: ligand / ID: 27 / Number of copies: 909 / 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

Concentration1 mg/mL
BufferpH: 8.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oy0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 375816
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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