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- EMDB-15621: RCII/PSI complex, focused refinement of PSI -

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Basic information

Entry
Database: EMDB / ID: EMD-15621
TitleRCII/PSI complex, focused refinement of PSI
Map data
Sample
  • Complex: RCII/PSI complex
    • Protein or peptide: x 9 types
  • Protein or peptide: x 2 types
  • Ligand: x 12 types
Keywordsphotosystem / assembly factor / membrane protein / 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 / electron transfer activity / oxidoreductase 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 / electron transfer activity / oxidoreductase 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 PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaB / 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 P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII / 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: 2.9 Å
AuthorsZhao Z / Vercellino I / Knoppova J / Sobotka R / Murray JW / Nixon PJ / Sazanov LA / Komenda J
Funding support United Kingdom, European Union, Czech Republic, 5 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L003260/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00931X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00931X/1 United Kingdom
European Research Council (ERC)854126European Union
Czech Science Foundation19-29225X Czech Republic
CitationJournal: Nat Commun / Year: 2023
Title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Authors: Ziyu Zhao / Irene Vercellino / Jana Knoppová / Roman Sobotka / James W Murray / Peter J Nixon / Leonid A Sazanov / Josef Komenda /
Abstract: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly ...Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising MnCaO cluster, thereby preventing the premature binding of Mn and Ca ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the MnCaO cluster.
History
DepositionAug 20, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15621.png

Downloads & links

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Map

FileDownload / File: emd_15621.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 400 pix.
= 488. Å		1.22 Å/pix.
x 400 pix.
= 488. Å		1.22 Å/pix.
x 400 pix.
= 488. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.077
Minimum - Maximum-0.117701255 - 0.52633595
Average (Standard dev.)-0.000004106279 (±0.009796271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 488.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15621_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15621_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RCII/PSI complex

EntireName: RCII/PSI complex
Components
  • Complex: RCII/PSI complex
    • 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 XII
  • Protein or peptide: Photosystem I reaction center subunit PsaK 1
  • Protein or peptide: Photosystem I reaction center subunit XI
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: beta,beta-carotene-4,4'-dione
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: beta,beta-caroten-4-one
  • 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: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: RCII/PSI complex

SupramoleculeName: RCII/PSI complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8, #11
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: His-D2/DeltaCP47

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 83.036398 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 81.369531 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGTLFHVAW QGNFEQWIKD PLNIRPIAH AIWDPHFGEG AVNAFTQAGA SNPVNIAYSG VYHWFYTIGM TTNQELYSGA VFLLVLASLF LFAGWLHLQP K FRPSLAWF ...String:
MATKFPKFSQ DLAQDPTTRR IWYGIATAHD FETHDGMTEE NLYQKIFASH FGHIAIIFLW TSGTLFHVAW QGNFEQWIKD PLNIRPIAH AIWDPHFGEG AVNAFTQAGA SNPVNIAYSG VYHWFYTIGM TTNQELYSGA VFLLVLASLF LFAGWLHLQP K FRPSLAWF KNAESRLNHH LAGLFGVSSL AWAGHLVHVA IPEARGQHVG WDNFLSTPPH PAGLMPFFTG NWGVYAADPD TA GHIFGTS EGAGTAILTF LGGFHPQTES LWLTDIAHHH LAIAVIFIIA GHMYRTNWGI GHSIKEILNA HKGPLTGAGH TNL YDTINN SLHFQLGLAL ASLGVITSLV AQHMYSLPSY AFIAQDHTTQ AALYTHHQYI AGFLMVGAFA HGAIFFVRDY DPVA NKDNV LARMLEHKEA LISHLSWVSL FLGFHTLGLY VHNDVVVAFG TPEKQILIEP VFAQWIQATS GKALYGFDVL LSNPD SIAS TTGAAWLPGW LDAINSGTNS LFLTIGPGDF LVHHAIALGL HTTALILIKG ALDARGSKLM PDKKDFGYSF PCDGPG RGG TCDISAWDAF YLAMFWMLNT LGWLTFYWHW KHLGVWSGNV AQFNENSTYL MGWFRDYLWA NSAQLINGYN PYGVNNL SV WAWMFLFGHL VWATGFMFLI SWRGYWQELI ETIVWAHERT PLANLVRWKD KPVALSIVQA RLVGLAHFTV GYVLTYAA F LIASTAGKFG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 8.837261 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 15.663749 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 8.154086 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 18.267082 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.414148 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.535415 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MDGLKSFLST APVMIMALLT FTAGILIEFN RFYPDLLFHP

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #9: Photosystem I reaction center subunit PsaK 1

MacromoleculeName: Photosystem I reaction center subunit PsaK 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 8.805451 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MHSFLLATAV PATLSWSPKV AGVMIACNIL AIAFGKLTIK QQNVGTPMPS SNFFGGFGLG AVLGTASFGH ILGAGVILGL ANMGVLGV

UniProtKB: Photosystem I reaction center subunit PsaK 1

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 16.631795 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.382063 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MALSDTQILA ALVVALLPAF LAFRLSTELY K

UniProtKB: Photosystem I reaction center subunit XII

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Macromolecule #12: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 12 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #13: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 13 / Number of copies: 95 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #14: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 14 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 17 / 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: 5 / 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: 4 / 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: 1 / Formula: 45D
Molecular weightTheoretical: 564.84 Da
Chemical component information

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

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Macromolecule #19: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 19 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 20 / Number of copies: 2 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

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

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Macromolecule #21: (3'R)-3'-hydroxy-beta,beta-caroten-4-one

MacromoleculeName: (3'R)-3'-hydroxy-beta,beta-caroten-4-one / type: ligand / ID: 21 / Number of copies: 1 / 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 #22: (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: 22 / Number of copies: 2 / 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 #23: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 23 / Number of copies: 1 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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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

Concentration0.2 mg/mL
BufferpH: 6.5
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2853 / Average electron dose: 90.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1250000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oy0


Details: 5oy0 for PSI
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 178513
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 80000 / Software - Name: RELION (ver. 3)
Details: 80000 particles on average were in the two good classes, while the residual junk only contained c.a. 15000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6wj6

chain_id: A, source_name: PDB, initial_model_type: experimental model

6wj6

chain_id: D, source_name: PDB, initial_model_type: experimental model

6wj6

chain_id: E, source_name: PDB, initial_model_type: experimental model

6wj6

chain_id: F, source_name: PDB, initial_model_type: experimental model

6wj6

chain_id: I, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: a, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: b, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: c, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: d, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: e, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: f, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: j, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: k, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: l, source_name: PDB, initial_model_type: experimental model

5oy0

chain_id: l, source_name: PDB, initial_model_type: experimental model

2xbg

chain_id: S, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Target criteria: Correlation coefficient
Output model

PDB-8asp:
RCII/PSI complex, focused refinement of PSI

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